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"gpu_samples": 0, "host": "cn604-12", "kind": "stage", "name": "all:tool_smcpp", "peak_rss_kib": 231796, "peak_rss_scope": "max single process among the child and its reaped descendants (wait4)", "schema": "bench_h2h.resources.v1", "slurm_job_id": "52021115", "stage_kind": "other", "start_utc": "2026-09-17T21:23:31.367383Z", "system_cpu_s": 6.645, "term_signal": null, "user_cpu_s": 11900.257, "wall_s": 1540.008} +{"cgroup": "/sys/fs/cgroup/system.slice/slurmstepd.scope/job_52021115", "cgroup_cpu_system_s": 17.359448, "cgroup_cpu_usage_s": 11969.214283, "cgroup_cpu_user_s": 11951.854834, "cgroup_memory_current_bytes": 40902656, "cgroup_memory_peak_bytes": 2518900736, "end_utc": "2026-09-17T21:49:11.411935Z", "exit_code": 0, "gpu_peak_memory_used_mib": null, "host": "cn604-12", "job_wall_s": 1576.762, "kind": "job_end", "schema": "bench_h2h.resources.v1", "slurm_job_id": "52021115", "stages_recorded": 7} diff --git a/estimates/smcpp_converged/a2/BOT_X100_20K/K1/g0/n32/smcpp/est/model.final.json b/estimates/smcpp_converged/a2/BOT_X100_20K/K1/g0/n32/smcpp/est/model.final.json new file mode 100644 index 0000000000000000000000000000000000000000..537e98c6b97a159fb74c77fe059fa8a5cdba83d7 --- /dev/null +++ b/estimates/smcpp_converged/a2/BOT_X100_20K/K1/g0/n32/smcpp/est/model.final.json @@ -0,0 +1,85 @@ +{ + "alpha": 100, + "hidden_states": { + "pop1": [ + 0.0, + 0.13273281592909533, + 0.14717693381168934, + 0.16504512165441051, + 0.19431107390572766, + 0.2349518836278101, + 0.3132040756687292, + 0.3713198073300181, + 0.4260983110118447, + 0.4789894310208009, + 0.5288545713465653, + 0.5859530250752629, + 0.6440495125875583, + 0.6762079558295799, + 0.7117706650843485, + 0.7716040081119574, + 0.824997741768265, + 0.9080803502010323, + 0.9733928145188007, + 1.0527003050617685, + 1.1097069606337668, + 1.1792437946917649, + 1.2499949146487008, + 1.3001002663332433, + 1.3999694637610618, + 1.4500158503542622, + 1.5065412318026135, + 1.6000285936341903, + 1.7000297528737338, + 1.800047526441973, + 1.9499893372367239, + 2.1500875847644867, + 2.677224957288915, + Infinity + ] + }, + "model": { + "N0": 3999.999953255611, + "class": "SMCModel", + "knots": [ + 0.13273281592909533, + 0.16504512165441051, + 0.2349518836278101, + 0.3713198073300181, + 0.4789894310208009, + 0.5859530250752629, + 0.6762079558295799, + 0.7716040081119574, + 0.9080803502010323, + 1.0527003050617685, + 1.1792437946917649, + 1.3001002663332433, + 1.4500158503542622, + 1.6000285936341903, + 1.800047526441973, + 2.1500875847644867 + ], + "pid": "pop1", + "spline_class": "Piecewise", + "y": [ + 0.9197240827152416, + 0.8820328853468826, + 0.8516692526759799, + 0.8351181185276507, + 0.8316178511021586, + 0.8333260633997936, + 0.8286166266690378, + 0.8040482942077363, + 0.7466593421908617, + 0.6474717973858176, + 0.5004662673925975, + 0.3008014496236371, + 0.04787522197154586, + -0.25386930323730217, + -0.5878495781116672, + -0.9313237996921986 + ] + }, + "rho": 7.999999857891455e-05, + "theta": 0.0001 +} \ No newline at end of file diff --git a/estimates/smcpp_converged/a2/BOT_X100_20K/K1/g0/n32/smcpp/estimate.cmd b/estimates/smcpp_converged/a2/BOT_X100_20K/K1/g0/n32/smcpp/estimate.cmd new file mode 100644 index 0000000000000000000000000000000000000000..71f51e7d9655b65283c1fab0df8853b36433065b --- /dev/null +++ b/estimates/smcpp_converged/a2/BOT_X100_20K/K1/g0/n32/smcpp/estimate.cmd @@ -0,0 +1 @@ +smc++ estimate --cores 8 --knots 16 --em-iterations 20 -o /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/smcpp/EQ/tune_d4_rp3_ftol1e-6/v2_a2_BOT_X100_20K/K1/g0/n32/smcpp/est --unfold -r 9.99999993922529e-09 --regularization-penalty 3.0 --ftol 1e-06 1.2500000146076218e-08 /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/smcpp/EQ/tune_d4_rp3_ftol1e-6/v2_a2_BOT_X100_20K/K1/g0/n32/smcpp/data/region_0.d0.smc.gz /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/smcpp/EQ/tune_d4_rp3_ftol1e-6/v2_a2_BOT_X100_20K/K1/g0/n32/smcpp/data/region_0.d1.smc.gz /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/smcpp/EQ/tune_d4_rp3_ftol1e-6/v2_a2_BOT_X100_20K/K1/g0/n32/smcpp/data/region_0.d2.smc.gz /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/smcpp/EQ/tune_d4_rp3_ftol1e-6/v2_a2_BOT_X100_20K/K1/g0/n32/smcpp/data/region_0.d3.smc.gz diff --git a/estimates/smcpp_converged/a2/BOT_X100_20K/K1/g0/n32/smcpp/estimate.err b/estimates/smcpp_converged/a2/BOT_X100_20K/K1/g0/n32/smcpp/estimate.err new file mode 100644 index 0000000000000000000000000000000000000000..b767ffa8ef07ae54e3c7060030825c672bfed49e --- /dev/null +++ b/estimates/smcpp_converged/a2/BOT_X100_20K/K1/g0/n32/smcpp/estimate.err @@ -0,0 +1,671 @@ +/ibex/sw/csi/smcpp/1.15.2/linux_binary/smcpp/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. + from ._conv import register_converters as _register_converters +496 smcpp.analysis.base INFO theta: 0.000100 +497 smcpp.analysis.base INFO rho: 0.000080 +497 smcpp.analysis.base WARNING Using unfolded SFS. The user should verify that the ancestral allele has been correctly coded. +497 smcpp.data_filter INFO Loading data... +550 smcpp.data_filter INFO 0.12 Gb of data +551 smcpp.data_filter INFO 1 population +/ibex/sw/csi/smcpp/1.15.2/linux_binary/smcpp/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. + from ._conv import register_converters as _register_converters +/ibex/sw/csi/smcpp/1.15.2/linux_binary/smcpp/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. + from ._conv import register_converters as _register_converters +/ibex/sw/csi/smcpp/1.15.2/linux_binary/smcpp/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. + from ._conv import register_converters as _register_converters +/ibex/sw/csi/smcpp/1.15.2/linux_binary/smcpp/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. + from ._conv import register_converters as _register_converters +3614 smcpp.optimize.plugins.progress_printer INFO Starting EM algorithm... +3614 smcpp.optimize.plugins.progress_printer INFO EM iteration 1 of 1... +3614 smcpp.analysis.base INFO Running E-step +3711 smcpp.analysis.base INFO E-step completed +3711 smcpp.optimize.plugins.loglikelihood_monitor INFO Loglik: -2501353.935020 +16789 smcpp.optimize.plugins.progress_printer INFO Current model: + + 1.02 0.73 0.24 -0.39 -1.05 -1.70 -2.35 -3.00 + 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.78 2.07 2.07 2.07 2.07 2.07 2.07 2.07 2.07 2.07 2.07 2.07 2.07 2.07 2.07 2.07 2.07 1.27 1.27 1.27 1.27 1.27 1.27 1.27 1.27 1.27 1.27 1.27 1.27 0.67 0.67 0.67 0.67 0.67 0.67 0.67 0.67 0.67 0.67 0.35 0.35 0.35 0.35 0.35 0.35 0.35 0.35 0.18 0.18 0.18 0.18 0.18 0.18 0.18 0.18 0.18 0.18 0.10 0.10 0.10 0.10 0.10 0.10 0.10 0.10 0.10 0.10 0.05 +16846 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 100000 +++-----+----+---+---+-+--+-+-+------------+------+----+---+---+++ + ++ + ++ + ++ Pop. 1 *******++ + ++ ++ + B********************* | + 10000 +++ B*********** +++ + ++ B******* ++ + ++ B****** ++ + ++ * ++ + 1000 +-+ B***** +-+ + ++ B****** ++ + ++ B******+ + ++ +* + ++ + +* + 100 +-+-----+----+---+---+-+--+-+-+------------+------+----+---+---+-+ + 10000 + Generations + + +16848 smcpp.data_filter INFO Loading data... +16966 smcpp.data_filter INFO 0.12 Gb of data +16967 smcpp.data_filter INFO 1 population +/ibex/sw/csi/smcpp/1.15.2/linux_binary/smcpp/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. + from ._conv import register_converters as _register_converters +/ibex/sw/csi/smcpp/1.15.2/linux_binary/smcpp/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. + from ._conv import register_converters as _register_converters +/ibex/sw/csi/smcpp/1.15.2/linux_binary/smcpp/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. + from ._conv import register_converters as _register_converters +/ibex/sw/csi/smcpp/1.15.2/linux_binary/smcpp/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. + from ._conv import register_converters as _register_converters +/ibex/sw/csi/smcpp/1.15.2/linux_binary/smcpp/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. + from ._conv import register_converters as _register_converters +/ibex/sw/csi/smcpp/1.15.2/linux_binary/smcpp/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. + from ._conv import register_converters as _register_converters +/ibex/sw/csi/smcpp/1.15.2/linux_binary/smcpp/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. + from ._conv import register_converters as _register_converters +/ibex/sw/csi/smcpp/1.15.2/linux_binary/smcpp/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. + from ._conv import register_converters as _register_converters +/ibex/sw/csi/smcpp/1.15.2/linux_binary/smcpp/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. + from ._conv import register_converters as _register_converters +/ibex/sw/csi/smcpp/1.15.2/linux_binary/smcpp/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. + from ._conv import register_converters as _register_converters +24304 smcpp.optimize.plugins.progress_printer INFO Starting EM algorithm... +24304 smcpp.optimize.plugins.progress_printer INFO EM iteration 1 of 20... +24304 smcpp.analysis.base INFO Running E-step +25693 smcpp.analysis.base INFO E-step completed +25694 smcpp.optimize.plugins.loglikelihood_monitor INFO Loglik: -159328.771153 +101733 smcpp.optimize.plugins.progress_printer INFO Current model: + + 0.59 0.55 0.55 0.55 0.56 0.56 0.55 0.50 0.39 0.22 0.25 0.16 -0.05 -0.33 -0.27 -0.31 + 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.80 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.75 1.75 1.75 1.75 1.75 1.75 1.75 1.75 1.75 1.75 1.75 1.75 1.73 1.73 1.73 1.73 1.73 1.65 1.65 1.65 1.65 1.65 1.65 1.47 1.47 1.47 1.47 1.47 1.25 1.25 1.25 1.25 1.28 1.28 1.28 1.28 1.17 1.17 1.17 0.96 0.96 0.96 0.96 0.72 0.72 0.72 0.72 0.76 0.76 0.76 0.76 0.76 0.76 0.74 +101741 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 10000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + ++ + ++ + B****B********B*********B*****B****B***B** Pop. 1 *******++ + ++ B***B*** ++ + ++ B**B** ++ + | B** | + ++ B** ++ + ++ * B**** + | B** | + | | + ++ ++ + | | + | | + | + | + 1000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + 10000 + Generations + + +101741 smcpp.optimize.plugins.progress_printer INFO EM iteration 2 of 20... +101741 smcpp.analysis.base INFO Running E-step +103337 smcpp.analysis.base INFO E-step completed +103340 smcpp.optimize.plugins.loglikelihood_monitor INFO New loglik: -159173.572695 (old: -159328.771153 [0.097408%]) +180717 smcpp.optimize.plugins.progress_printer INFO Current model: + + 0.80 0.77 0.75 0.76 0.76 0.76 0.74 0.69 0.60 0.48 0.39 0.34 0.15 -0.07 -0.18 -0.08 + 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.12 2.12 2.12 2.12 2.12 2.12 2.12 2.12 2.12 2.12 2.12 2.12 2.12 2.12 2.12 2.12 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.10 2.10 2.10 2.10 2.10 2.00 2.00 2.00 2.00 2.00 2.00 1.82 1.82 1.82 1.82 1.82 1.62 1.62 1.62 1.62 1.47 1.47 1.47 1.47 1.40 1.40 1.40 1.16 1.16 1.16 1.16 0.93 0.93 0.93 0.93 0.83 0.83 0.83 0.83 0.83 0.83 0.92 +180740 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 10000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + B****B********B*********B*****B****B***B**B*** + ++ + ++ B*** Pop. 1 *******++ + ++ B**B** ++ + ++ B** ++ + | B** | + ++ B** +* + ++ B***+ + | | + | | + ++ ++ + | | + | | + | + | + 1000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + 10000 + Generations + + +180741 smcpp.optimize.plugins.progress_printer INFO EM iteration 3 of 20... +180741 smcpp.analysis.base INFO Running E-step +182658 smcpp.analysis.base INFO E-step completed +182661 smcpp.optimize.plugins.loglikelihood_monitor INFO New loglik: -159148.124505 (old: -159173.572695 [0.015988%]) +261225 smcpp.optimize.plugins.progress_printer INFO Current model: + + 0.68 0.63 0.62 0.62 0.63 0.62 0.60 0.56 0.47 0.36 0.25 0.16 0.02 -0.20 -0.37 -0.47 + 1.97 1.97 1.97 1.97 1.97 1.97 1.97 1.97 1.88 1.88 1.88 1.88 1.88 1.88 1.88 1.88 1.88 1.88 1.88 1.88 1.88 1.85 1.85 1.85 1.85 1.85 1.85 1.85 1.85 1.85 1.85 1.85 1.85 1.85 1.85 1.85 1.85 1.86 1.86 1.86 1.86 1.86 1.86 1.86 1.86 1.86 1.87 1.87 1.87 1.87 1.87 1.87 1.87 1.86 1.86 1.86 1.86 1.86 1.83 1.83 1.83 1.83 1.83 1.74 1.74 1.74 1.74 1.74 1.74 1.60 1.60 1.60 1.60 1.60 1.44 1.44 1.44 1.44 1.29 1.29 1.29 1.29 1.17 1.17 1.17 1.02 1.02 1.02 1.02 0.82 0.82 0.82 0.82 0.69 0.69 0.69 0.69 0.69 0.69 0.63 +261276 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 10000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + B***** + ++ + ++ B********B*********B*****B****B***B**B*** Pop. 1 *******++ + ++ B**B** ++ + ++ B** ++ + | B**B** | + ++ * ++ + ++ B** ++ + | B**** + | | + ++ ++ + | | + | | + | + | + 1000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + 10000 + Generations + + +261277 smcpp.optimize.plugins.progress_printer INFO EM iteration 4 of 20... +261277 smcpp.analysis.base INFO Running E-step +262868 smcpp.analysis.base INFO E-step completed +262871 smcpp.optimize.plugins.loglikelihood_monitor INFO New loglik: -159130.059270 (old: -159148.124505 [0.011351%]) +339350 smcpp.optimize.plugins.progress_printer INFO Current model: + + 0.82 0.78 0.76 0.76 0.77 0.77 0.75 0.70 0.62 0.52 0.40 0.28 0.14 -0.06 -0.27 -0.45 + 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.19 2.19 2.19 2.19 2.19 2.19 2.19 2.19 2.19 2.19 2.19 2.19 2.19 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.16 2.16 2.16 2.16 2.16 2.16 2.16 2.15 2.15 2.15 2.15 2.15 2.11 2.11 2.11 2.11 2.11 2.01 2.01 2.01 2.01 2.01 2.01 1.86 1.86 1.86 1.86 1.86 1.67 1.67 1.67 1.67 1.50 1.50 1.50 1.50 1.33 1.33 1.33 1.15 1.15 1.15 1.15 0.94 0.94 0.94 0.94 0.76 0.76 0.76 0.76 0.76 0.76 0.64 +339400 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 10000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + B****B********B*********B*****B****B***B**B*** + ++ + ++ B**B**op. 1 *******++ + ++ B** ++ + ++ B** ++ + | B** | + ++ B** ++ + ++ B***+ + | * + | | + ++ ++ + | | + | | + | + | + 1000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + 10000 + Generations + + +339400 smcpp.optimize.plugins.progress_printer INFO EM iteration 5 of 20... +339400 smcpp.analysis.base INFO Running E-step +340977 smcpp.analysis.base INFO E-step completed +340981 smcpp.optimize.plugins.loglikelihood_monitor INFO New loglik: -159123.551298 (old: -159130.059270 [0.004090%]) +416121 smcpp.optimize.plugins.progress_printer INFO Current model: + + 0.77 0.72 0.70 0.69 0.70 0.70 0.68 0.63 0.56 0.46 0.34 0.21 0.06 -0.14 -0.37 -0.60 + 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.06 2.06 2.06 2.06 2.06 2.06 2.06 2.06 2.06 2.06 2.06 2.06 2.06 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.01 2.01 2.01 2.01 2.01 2.01 2.01 2.01 2.01 2.01 2.01 2.01 1.97 1.97 1.97 1.97 1.97 1.88 1.88 1.88 1.88 1.88 1.88 1.75 1.75 1.75 1.75 1.75 1.58 1.58 1.58 1.58 1.41 1.41 1.41 1.41 1.24 1.24 1.24 1.06 1.06 1.06 1.06 0.87 0.87 0.87 0.87 0.69 0.69 0.69 0.69 0.69 0.69 0.55 +416154 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 10000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + B****B********B*********B*****B****B***B** + ++ + ++ B***B*** Pop. 1 *******++ + ++ B** ++ + ++ B*B** ++ + | B** | + ++ B** ++ + ++ * ++ + | B***| + | * + ++ ++ + | | + | | + | + | + 1000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + 10000 + Generations + + +416155 smcpp.optimize.plugins.progress_printer INFO EM iteration 6 of 20... +416155 smcpp.analysis.base INFO Running E-step +417693 smcpp.analysis.base INFO E-step completed +417696 smcpp.optimize.plugins.loglikelihood_monitor INFO New loglik: -159120.634024 (old: -159123.551298 [0.001833%]) +491267 smcpp.optimize.plugins.progress_printer INFO Current model: + + 0.83 0.79 0.76 0.75 0.76 0.76 0.74 0.70 0.63 0.53 0.41 0.27 0.11 -0.09 -0.33 -0.59 + 2.30 2.30 2.30 2.30 2.30 2.30 2.30 2.30 2.20 2.20 2.20 2.20 2.20 2.20 2.20 2.20 2.20 2.20 2.20 2.20 2.20 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.13 2.13 2.13 2.13 2.13 2.13 2.13 2.13 2.13 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.10 2.10 2.10 2.10 2.10 2.01 2.01 2.01 2.01 2.01 2.01 1.87 1.87 1.87 1.87 1.87 1.69 1.69 1.69 1.69 1.50 1.50 1.50 1.50 1.31 1.31 1.31 1.11 1.11 1.11 1.11 0.91 0.91 0.91 0.91 0.72 0.72 0.72 0.72 0.72 0.72 0.56 +491286 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 10000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + B****B********B*********B*****B****B***B**B*** + ++ + ++ B**B**op. 1 *******++ + ++ B** ++ + ++ B** ++ + | B** | + ++ B** ++ + ++ * ++ + | B***| + | * + ++ ++ + | | + | | + | + | + 1000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + 10000 + Generations + + +491287 smcpp.optimize.plugins.progress_printer INFO EM iteration 7 of 20... +491287 smcpp.analysis.base INFO Running E-step +492792 smcpp.analysis.base INFO E-step completed +492795 smcpp.optimize.plugins.loglikelihood_monitor INFO New loglik: -159118.625487 (old: -159120.634024 [0.001262%]) +566572 smcpp.optimize.plugins.progress_printer INFO Current model: + + 0.81 0.77 0.74 0.73 0.73 0.73 0.72 0.67 0.60 0.50 0.38 0.24 0.07 -0.14 -0.38 -0.64 + 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.09 2.09 2.09 2.09 2.09 2.09 2.09 2.09 2.09 2.09 2.09 2.09 2.09 2.09 2.09 2.09 2.07 2.07 2.07 2.07 2.07 2.07 2.07 2.07 2.07 2.08 2.08 2.08 2.08 2.08 2.08 2.08 2.08 2.08 2.08 2.08 2.08 2.05 2.05 2.05 2.05 2.05 1.96 1.96 1.96 1.96 1.96 1.96 1.83 1.83 1.83 1.83 1.83 1.66 1.66 1.66 1.66 1.47 1.47 1.47 1.47 1.27 1.27 1.27 1.07 1.07 1.07 1.07 0.87 0.87 0.87 0.87 0.68 0.68 0.68 0.68 0.68 0.68 0.53 +566580 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 10000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + B****B********B*********B*****B****B***B**B*** + ++ + ++ B*** Pop. 1 *******++ + ++ B**B** ++ + ++ B** ++ + | B** | + ++ B** ++ + ++ * ++ + | B***| + | * + ++ ++ + | | + | | + | + | + 1000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + 10000 + Generations + + +566581 smcpp.optimize.plugins.progress_printer INFO EM iteration 8 of 20... +566581 smcpp.analysis.base INFO Running E-step +568098 smcpp.analysis.base INFO E-step completed +568101 smcpp.optimize.plugins.loglikelihood_monitor INFO New loglik: -159117.206220 (old: -159118.625487 [0.000892%]) +642119 smcpp.optimize.plugins.progress_printer INFO Current model: + + 0.84 0.80 0.77 0.76 0.76 0.76 0.75 0.71 0.64 0.54 0.41 0.27 0.08 -0.13 -0.38 -0.65 + 2.32 2.32 2.32 2.32 2.32 2.32 2.32 2.32 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.13 2.13 2.13 2.13 2.13 2.13 2.13 2.13 2.13 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.11 2.11 2.11 2.11 2.11 2.03 2.03 2.03 2.03 2.03 2.03 1.89 1.89 1.89 1.89 1.89 1.71 1.71 1.71 1.71 1.51 1.51 1.51 1.51 1.30 1.30 1.30 1.09 1.09 1.09 1.09 0.88 0.88 0.88 0.88 0.68 0.68 0.68 0.68 0.68 0.68 0.52 +642151 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 10000 B*****---------+---------+-----+-----+---+---+--+--+-+----------+-+ + ++ B********B*********B*****B****B***B**B*** + ++ + ++ B**B**op. 1 *******++ + ++ B** ++ + ++ B** ++ + | B** | + ++ B** ++ + ++ * ++ + | B***| + | * + ++ +* + | | + | | + | + | + 1000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + 10000 + Generations + + +642152 smcpp.optimize.plugins.progress_printer INFO EM iteration 9 of 20... +642152 smcpp.analysis.base INFO Running E-step +643774 smcpp.analysis.base INFO E-step completed +643776 smcpp.optimize.plugins.loglikelihood_monitor INFO New loglik: -159115.725240 (old: -159117.206220 [0.000931%]) +722751 smcpp.optimize.plugins.progress_printer INFO Current model: + + 0.84 0.79 0.76 0.75 0.75 0.75 0.74 0.70 0.63 0.54 0.41 0.26 0.07 -0.16 -0.41 -0.68 + 2.31 2.31 2.31 2.31 2.31 2.31 2.31 2.31 2.21 2.21 2.21 2.21 2.21 2.21 2.21 2.21 2.21 2.21 2.21 2.21 2.21 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.14 2.12 2.12 2.12 2.12 2.12 2.12 2.12 2.12 2.12 2.12 2.12 2.12 2.12 2.12 2.12 2.12 2.13 2.13 2.13 2.13 2.13 2.10 2.10 2.10 2.10 2.10 2.02 2.02 2.02 2.02 2.02 2.02 1.88 1.88 1.88 1.88 1.88 1.71 1.71 1.71 1.71 1.51 1.51 1.51 1.51 1.29 1.29 1.29 1.07 1.07 1.07 1.07 0.85 0.85 0.85 0.85 0.66 0.66 0.66 0.66 0.66 0.66 0.50 +722787 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 10000 B*****---------+---------+-----+-----+---+---+--+--+-+----------+-+ + ++ B********B*********B*****B****B***B**B*** + ++ + ++ B**B**op. 1 *******++ + ++ B** ++ + ++ B** ++ + | B** | + ++ * ++ + ++ B** ++ + | B***| + | * + ++ +* + | | + | | + | + | + 1000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + 10000 + Generations + + +722788 smcpp.optimize.plugins.progress_printer INFO EM iteration 10 of 20... +722788 smcpp.analysis.base INFO Running E-step +724393 smcpp.analysis.base INFO E-step completed +724395 smcpp.optimize.plugins.loglikelihood_monitor INFO New loglik: -159114.421104 (old: -159115.725240 [0.000820%]) +800655 smcpp.optimize.plugins.progress_printer INFO Current model: + + 0.86 0.81 0.78 0.77 0.77 0.77 0.76 0.72 0.65 0.55 0.43 0.27 0.07 -0.16 -0.42 -0.70 + 2.35 2.35 2.35 2.35 2.35 2.35 2.35 2.35 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.16 2.16 2.16 2.16 2.16 2.13 2.13 2.13 2.13 2.13 2.05 2.05 2.05 2.05 2.05 2.05 1.92 1.92 1.92 1.92 1.92 1.74 1.74 1.74 1.74 1.53 1.53 1.53 1.53 1.31 1.31 1.31 1.08 1.08 1.08 1.08 0.85 0.85 0.85 0.85 0.65 0.65 0.65 0.65 0.65 0.65 0.50 +800695 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 10000 B*****---------+---------+-----+-----+---+---+--+--+-+----------+-+ + ++ B********B*********B*****B****B***B**B*** + ++ + ++ B**B**op. 1 *******++ + ++ B** ++ + ++ B** ++ + | B** | + ++ * ++ + ++ B** ++ + | B***| + | * + ++ +* + | | + | | + | + | + 1000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + 10000 + Generations + + +800696 smcpp.optimize.plugins.progress_printer INFO EM iteration 11 of 20... +800696 smcpp.analysis.base INFO Running E-step +802226 smcpp.analysis.base INFO E-step completed +802229 smcpp.optimize.plugins.loglikelihood_monitor INFO New loglik: -159113.109404 (old: -159114.421104 [0.000824%]) +875453 smcpp.optimize.plugins.progress_printer INFO Current model: + + 0.86 0.81 0.78 0.77 0.77 0.77 0.76 0.72 0.66 0.56 0.43 0.27 0.06 -0.18 -0.45 -0.73 + 2.36 2.36 2.36 2.36 2.36 2.36 2.36 2.36 2.26 2.26 2.26 2.26 2.26 2.26 2.26 2.26 2.26 2.26 2.26 2.26 2.26 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.15 2.16 2.16 2.16 2.16 2.16 2.16 2.16 2.16 2.16 2.16 2.16 2.16 2.14 2.14 2.14 2.14 2.14 2.06 2.06 2.06 2.06 2.06 2.06 1.93 1.93 1.93 1.93 1.93 1.75 1.75 1.75 1.75 1.54 1.54 1.54 1.54 1.31 1.31 1.31 1.07 1.07 1.07 1.07 0.84 0.84 0.84 0.84 0.64 0.64 0.64 0.64 0.64 0.64 0.48 +875471 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 10000 B*****---------+---------+-----+-----+---+---+--+--+-+----------+-+ + ++ B********B*********B*****B****B***B**B*** + ++ + ++ B**B**op. 1 *******++ + ++ B** ++ + ++ B** ++ + | B** | + ++ * ++ + ++ B** ++ + | B***| + | * + ++ +* + | | + | | + | + | + 1000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + 10000 + Generations + + +875471 smcpp.optimize.plugins.progress_printer INFO EM iteration 12 of 20... +875471 smcpp.analysis.base INFO Running E-step +876967 smcpp.analysis.base INFO E-step completed +876969 smcpp.optimize.plugins.loglikelihood_monitor INFO New loglik: -159111.892794 (old: -159113.109404 [0.000765%]) +949583 smcpp.optimize.plugins.progress_printer INFO Current model: + + 0.87 0.83 0.79 0.78 0.78 0.78 0.77 0.74 0.67 0.57 0.44 0.27 0.06 -0.18 -0.46 -0.75 + 2.39 2.39 2.39 2.39 2.39 2.39 2.39 2.39 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.21 2.21 2.21 2.21 2.21 2.21 2.21 2.21 2.21 2.21 2.21 2.21 2.21 2.21 2.21 2.21 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.18 2.16 2.16 2.16 2.16 2.16 2.09 2.09 2.09 2.09 2.09 2.09 1.96 1.96 1.96 1.96 1.96 1.77 1.77 1.77 1.77 1.56 1.56 1.56 1.56 1.31 1.31 1.31 1.07 1.07 1.07 1.07 0.83 0.83 0.83 0.83 0.63 0.63 0.63 0.63 0.63 0.63 0.47 +949617 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 10000 B*****---------+---------+-----+-----+---+---+--+--+-+----------+-+ + ++ B********B*********B*****B****B***B**B***B*** + ++ + ++ B**op. 1 *******++ + ++ B** ++ + ++ B** ++ + | B** | + ++ * ++ + ++ B** ++ + | B***| + | * + ++ +* + | | + | | + | + | + 1000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + 10000 + Generations + + +949618 smcpp.optimize.plugins.progress_printer INFO EM iteration 13 of 20... +949618 smcpp.analysis.base INFO Running E-step +951109 smcpp.analysis.base INFO E-step completed +951112 smcpp.optimize.plugins.loglikelihood_monitor INFO New loglik: -159110.706990 (old: -159111.892794 [0.000745%]) +1023201 smcpp.optimize.plugins.progress_printer INFO Current model: + + 0.88 0.83 0.80 0.78 0.78 0.78 0.78 0.74 0.68 0.58 0.45 0.28 0.06 -0.20 -0.48 -0.78 + 2.40 2.40 2.40 2.40 2.40 2.40 2.40 2.40 2.30 2.30 2.30 2.30 2.30 2.30 2.30 2.30 2.30 2.30 2.30 2.30 2.30 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.19 2.19 2.19 2.19 2.19 2.19 2.19 2.19 2.19 2.19 2.19 2.19 2.19 2.19 2.19 2.19 2.19 2.19 2.19 2.19 2.19 2.17 2.17 2.17 2.17 2.17 2.10 2.10 2.10 2.10 2.10 2.10 1.97 1.97 1.97 1.97 1.97 1.79 1.79 1.79 1.79 1.57 1.57 1.57 1.57 1.32 1.32 1.32 1.06 1.06 1.06 1.06 0.82 0.82 0.82 0.82 0.62 0.62 0.62 0.62 0.62 0.62 0.46 +1023239 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 10000 B*****---------+---------+-----+-----+---+---+--+--+-+----------+-+ + ++ B********B*********B*****B****B***B**B***B*** + ++ + ++ B**op. 1 *******++ + ++ B** ++ + ++ B** ++ + | B** | + ++ * ++ + ++ B** ++ + | B***| + | * + ++ +* + | | + | | + | + | + 1000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + 10000 + Generations + + +1023240 smcpp.optimize.plugins.progress_printer INFO EM iteration 14 of 20... +1023240 smcpp.analysis.base INFO Running E-step +1024712 smcpp.analysis.base INFO E-step completed +1024716 smcpp.optimize.plugins.loglikelihood_monitor INFO New loglik: -159109.589487 (old: -159110.706990 [0.000702%]) +1096123 smcpp.optimize.plugins.progress_printer INFO Current model: + + 0.88 0.84 0.81 0.79 0.79 0.79 0.78 0.75 0.69 0.59 0.46 0.28 0.06 -0.20 -0.50 -0.80 + 2.42 2.42 2.42 2.42 2.42 2.42 2.42 2.42 2.32 2.32 2.32 2.32 2.32 2.32 2.32 2.32 2.32 2.32 2.32 2.32 2.32 2.24 2.24 2.24 2.24 2.24 2.24 2.24 2.24 2.24 2.24 2.24 2.24 2.24 2.24 2.24 2.24 2.21 2.21 2.21 2.21 2.21 2.21 2.21 2.21 2.21 2.20 2.20 2.20 2.20 2.20 2.20 2.20 2.21 2.21 2.21 2.21 2.21 2.19 2.19 2.19 2.19 2.19 2.12 2.12 2.12 2.12 2.12 2.12 2.00 2.00 2.00 2.00 2.00 1.81 1.81 1.81 1.81 1.58 1.58 1.58 1.58 1.32 1.32 1.32 1.06 1.06 1.06 1.06 0.82 0.82 0.82 0.82 0.61 0.61 0.61 0.61 0.61 0.61 0.45 +1096157 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 10000 B****B********-+---------+-----+-----+---+---+--+--+-+----------+-+ + ++ B*********B*****B****B***B**B***B*** + ++ + ++ B**op. 1 *******++ + ++ B** ++ + ++ B** ++ + | B** | + ++ * ++ + ++ B** ++ + | * | + | B***| + ++ +* + | | + | | + | + | + 1000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + 10000 + Generations + + +1096158 smcpp.optimize.plugins.progress_printer INFO EM iteration 15 of 20... +1096158 smcpp.analysis.base INFO Running E-step +1097623 smcpp.analysis.base INFO E-step completed +1097627 smcpp.optimize.plugins.loglikelihood_monitor INFO New loglik: -159108.517601 (old: -159109.589487 [0.000674%]) +1168299 smcpp.optimize.plugins.progress_printer INFO Current model: + + 0.89 0.85 0.82 0.80 0.80 0.80 0.79 0.76 0.70 0.60 0.46 0.28 0.06 -0.21 -0.51 -0.82 + 2.44 2.44 2.44 2.44 2.44 2.44 2.44 2.44 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.26 2.26 2.26 2.26 2.26 2.26 2.26 2.26 2.26 2.26 2.26 2.26 2.26 2.26 2.26 2.26 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.22 2.21 2.21 2.21 2.21 2.21 2.14 2.14 2.14 2.14 2.14 2.14 2.01 2.01 2.01 2.01 2.01 1.83 1.83 1.83 1.83 1.59 1.59 1.59 1.59 1.33 1.33 1.33 1.06 1.06 1.06 1.06 0.81 0.81 0.81 0.81 0.60 0.60 0.60 0.60 0.60 0.60 0.44 +1168319 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 10000 B****B********-+---------+-----+-----+---+---+--+--+-+----------+-+ + ++ B*********B*****B****B***B**B***B*** + ++ + ++ B**op. 1 *******++ + ++ B** ++ + ++ B** ++ + | B** | + ++ * ++ + ++ B** ++ + | * | + | B***| + ++ +* + | * + | | + | + | + 1000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + 10000 + Generations + + +1168319 smcpp.optimize.plugins.progress_printer INFO EM iteration 16 of 20... +1168319 smcpp.analysis.base INFO Running E-step +1169776 smcpp.analysis.base INFO E-step completed +1169778 smcpp.optimize.plugins.loglikelihood_monitor INFO New loglik: -159107.504982 (old: -159108.517601 [0.000636%]) +1240096 smcpp.optimize.plugins.progress_printer INFO Current model: + + 0.90 0.86 0.82 0.81 0.80 0.81 0.80 0.77 0.71 0.61 0.47 0.29 0.05 -0.22 -0.53 -0.85 + 2.45 2.45 2.45 2.45 2.45 2.45 2.45 2.45 2.35 2.35 2.35 2.35 2.35 2.35 2.35 2.35 2.35 2.35 2.35 2.35 2.35 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.24 2.24 2.24 2.24 2.24 2.24 2.24 2.24 2.24 2.23 2.23 2.23 2.23 2.23 2.23 2.23 2.24 2.24 2.24 2.24 2.24 2.22 2.22 2.22 2.22 2.22 2.16 2.16 2.16 2.16 2.16 2.16 2.03 2.03 2.03 2.03 2.03 1.84 1.84 1.84 1.84 1.60 1.60 1.60 1.60 1.33 1.33 1.33 1.06 1.06 1.06 1.06 0.80 0.80 0.80 0.80 0.59 0.59 0.59 0.59 0.59 0.59 0.43 +1240109 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 10000 B****B********-+---------+-----+-----+---+---+--+--+-+----------+-+ + ++ B*********B*****B****B***B**B***B*** + ++ + ++ B**op. 1 *******++ + ++ B** ++ + ++ B** ++ + | B** | + ++ * ++ + ++ B** ++ + | * | + | B***| + ++ +* + | * + | | + | + | + 1000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + 10000 + Generations + + +1240110 smcpp.optimize.plugins.progress_printer INFO EM iteration 17 of 20... +1240110 smcpp.analysis.base INFO Running E-step +1241557 smcpp.analysis.base INFO E-step completed +1241559 smcpp.optimize.plugins.loglikelihood_monitor INFO New loglik: -159106.539274 (old: -159107.504982 [0.000607%]) +1312348 smcpp.optimize.plugins.progress_printer INFO Current model: + + 0.90 0.86 0.83 0.81 0.81 0.81 0.81 0.78 0.72 0.62 0.48 0.29 0.05 -0.23 -0.54 -0.87 + 2.47 2.47 2.47 2.47 2.47 2.47 2.47 2.47 2.37 2.37 2.37 2.37 2.37 2.37 2.37 2.37 2.37 2.37 2.37 2.37 2.37 2.29 2.29 2.29 2.29 2.29 2.29 2.29 2.29 2.29 2.29 2.29 2.29 2.29 2.29 2.29 2.29 2.26 2.26 2.26 2.26 2.26 2.26 2.26 2.26 2.26 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.25 2.24 2.24 2.24 2.24 2.24 2.18 2.18 2.18 2.18 2.18 2.18 2.05 2.05 2.05 2.05 2.05 1.86 1.86 1.86 1.86 1.62 1.62 1.62 1.62 1.34 1.34 1.34 1.05 1.05 1.05 1.05 0.79 0.79 0.79 0.79 0.58 0.58 0.58 0.58 0.58 0.58 0.42 +1312361 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 10000 B****B********-+---------+-----+-----+---+---+--+--+-+----------+-+ + ++ B*********B*****B****B***B**B***B*** + ++ + ++ B**op. 1 *******++ + ++ B** ++ + ++ B** ++ + | B** | + ++ * ++ + ++ B** ++ + | * | + | B***| + ++ +* + | * + | | + | + | + 1000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + 10000 + Generations + + +1312361 smcpp.optimize.plugins.progress_printer INFO EM iteration 18 of 20... +1312361 smcpp.analysis.base INFO Running E-step +1313838 smcpp.analysis.base INFO E-step completed +1313840 smcpp.optimize.plugins.loglikelihood_monitor INFO New loglik: -159105.623395 (old: -159106.539274 [0.000576%]) +1380764 smcpp.optimize.plugins.progress_printer INFO Current model: + + 0.91 0.87 0.84 0.82 0.82 0.82 0.81 0.79 0.73 0.63 0.49 0.29 0.05 -0.24 -0.56 -0.89 + 2.48 2.48 2.48 2.48 2.48 2.48 2.48 2.48 2.39 2.39 2.39 2.39 2.39 2.39 2.39 2.39 2.39 2.39 2.39 2.39 2.39 2.31 2.31 2.31 2.31 2.31 2.31 2.31 2.31 2.31 2.31 2.31 2.31 2.31 2.31 2.31 2.31 2.27 2.27 2.27 2.27 2.27 2.27 2.27 2.27 2.27 2.27 2.27 2.27 2.27 2.27 2.27 2.27 2.27 2.27 2.27 2.27 2.27 2.26 2.26 2.26 2.26 2.26 2.20 2.20 2.20 2.20 2.20 2.20 2.07 2.07 2.07 2.07 2.07 1.88 1.88 1.88 1.88 1.63 1.63 1.63 1.63 1.34 1.34 1.34 1.05 1.05 1.05 1.05 0.79 0.79 0.79 0.79 0.57 0.57 0.57 0.57 0.57 0.57 0.41 +1380772 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 10000 B****B********B**********+-----+-----+---+---+--+--+-+----------+-+ + ++ B*****B****B***B**B***B*** + ++ + ++ B**op. 1 *******++ + ++ B** ++ + ++ B** ++ + | B** | + ++ * ++ + ++ B** ++ + | * | + | B***| + ++ +* + | * + | | + | + | + 1000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + 10000 + Generations + + +1380772 smcpp.optimize.plugins.progress_printer INFO EM iteration 19 of 20... +1380772 smcpp.analysis.base INFO Running E-step +1382384 smcpp.analysis.base INFO E-step completed +1382387 smcpp.optimize.plugins.loglikelihood_monitor INFO New loglik: -159104.752287 (old: -159105.623395 [0.000548%]) +1448946 smcpp.optimize.plugins.progress_printer INFO Current model: + + 0.91 0.88 0.84 0.83 0.82 0.83 0.82 0.80 0.74 0.64 0.49 0.30 0.05 -0.25 -0.57 -0.91 + 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.40 2.40 2.40 2.40 2.40 2.40 2.40 2.40 2.40 2.40 2.40 2.40 2.40 2.33 2.33 2.33 2.33 2.33 2.33 2.33 2.33 2.33 2.33 2.33 2.33 2.33 2.33 2.33 2.33 2.29 2.29 2.29 2.29 2.29 2.29 2.29 2.29 2.29 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.28 2.27 2.27 2.27 2.27 2.27 2.22 2.22 2.22 2.22 2.22 2.22 2.09 2.09 2.09 2.09 2.09 1.89 1.89 1.89 1.89 1.64 1.64 1.64 1.64 1.35 1.35 1.35 1.05 1.05 1.05 1.05 0.78 0.78 0.78 0.78 0.56 0.56 0.56 0.56 0.56 0.56 0.40 +1448956 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 10000 B****B********B**********+-----+-----+---+---+--+--+-+----------+-+ + ++ B*****B****B***B**B***B*** + ++ + ++ B**op. 1 *******++ + ++ B** ++ + ++ B** ++ + | B** | + ++ * ++ + ++ B** ++ + | * | + | B***| + ++ +* + | * + | | + | + | + 1000 +-+------------+---------+-----+-----+---+---+--+--+-+----------+-+ + 10000 + Generations + + +1448957 smcpp.optimize.plugins.progress_printer INFO EM iteration 20 of 20... +1448957 smcpp.analysis.base INFO Running E-step +1450348 smcpp.analysis.base INFO E-step completed +1450351 smcpp.optimize.plugins.loglikelihood_monitor INFO New loglik: -159103.925895 (old: -159104.752287 [0.000519%]) +1517112 smcpp.optimize.plugins.progress_printer INFO Current model: + + 0.92 0.88 0.85 0.84 0.83 0.83 0.83 0.80 0.75 0.65 0.50 0.30 0.05 -0.25 -0.59 -0.93 + 2.51 2.51 2.51 2.51 2.51 2.51 2.51 2.51 2.42 2.42 2.42 2.42 2.42 2.42 2.42 2.42 2.42 2.42 2.42 2.42 2.42 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.34 2.31 2.31 2.31 2.31 2.31 2.31 2.31 2.31 2.31 2.30 2.30 2.30 2.30 2.30 2.30 2.30 2.30 2.30 2.30 2.30 2.30 2.29 2.29 2.29 2.29 2.29 2.23 2.23 2.23 2.23 2.23 2.23 2.11 2.11 2.11 2.11 2.11 1.91 1.91 1.91 1.91 1.65 1.65 1.65 1.65 1.35 1.35 1.35 1.05 1.05 1.05 1.05 0.78 0.78 0.78 0.78 0.56 0.56 0.56 0.56 0.56 0.56 0.39 +1517145 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 100000 +++------------+--------+------+----+---+---+--+--+-+----------+++ + ++ + ++ + ++ Pop. 1 *******++ + ++ ++ + ++ ++ + ++ ++ + | | + 10000 B****B*******B**********B*****B****B**B**B**** +++ + ++ B**B**B** ++ + ++ B** ++ + ++ B** ++ + ++ B** ++ + ++ B***+ + | + * + 1000 +-+------------+--------+------+----+---+---+--+--+-+----------+-+ + 10000 + Generations + + diff --git a/estimates/smcpp_converged/a2/BOT_X100_20K/K1/g0/n32/smcpp/estimate.out b/estimates/smcpp_converged/a2/BOT_X100_20K/K1/g0/n32/smcpp/estimate.out new file mode 100644 index 0000000000000000000000000000000000000000..ca0c0be44bf1856a843a6d08528f6530ff890e63 --- /dev/null +++ b/estimates/smcpp_converged/a2/BOT_X100_20K/K1/g0/n32/smcpp/estimate.out @@ -0,0 +1,87 @@ +RUNNING THE L-BFGS-B CODE + + * * * + +Machine precision = 2.220D-16 + N = 8 M = 10 + +At X0 0 variables are exactly at the bounds + +At iterate 0 f= 2.47563D+06 |proj g|= 3.00000D+00 + +At iterate 1 f= 2.43192D+06 |proj g|= 3.66793D+00 + +At iterate 2 f= 2.42556D+06 |proj g|= 3.50958D+00 + +At iterate 3 f= 2.42106D+06 |proj g|= 4.08788D+00 + +At iterate 4 f= 2.42048D+06 |proj g|= 4.03008D+00 + +At iterate 5 f= 2.42026D+06 |proj g|= 3.16319D+00 + +At iterate 6 f= 2.41996D+06 |proj g|= 3.23734D+00 + +At iterate 7 f= 2.41974D+06 |proj g|= 3.27927D+00 + +At iterate 8 f= 2.41963D+06 |proj g|= 3.66470D+00 + +At iterate 9 f= 2.41952D+06 |proj g|= 4.02723D+00 + +At iterate 10 f= 2.41950D+06 |proj g|= 4.02351D+00 + +At iterate 11 f= 2.41949D+06 |proj g|= 4.02288D+00 + +At iterate 12 f= 2.41947D+06 |proj g|= 3.49064D+00 + +At iterate 13 f= 2.41942D+06 |proj g|= 3.56480D+00 + +At iterate 14 f= 2.41929D+06 |proj g|= 3.84042D+00 + +At iterate 15 f= 2.41907D+06 |proj g|= 4.65678D+00 + Positive dir derivative in projection + Using the backtracking step + +At iterate 16 f= 2.41905D+06 |proj g|= 4.90374D+00 + +At iterate 17 f= 2.41888D+06 |proj g|= 5.43762D+00 + +At iterate 18 f= 2.41886D+06 |proj g|= 5.39769D+00 + +At iterate 19 f= 2.41885D+06 |proj g|= 6.00000D+00 + +At iterate 20 f= 2.41885D+06 |proj g|= 5.37733D+00 + +At iterate 21 f= 2.41885D+06 |proj g|= 5.36758D+00 + +At iterate 22 f= 2.41885D+06 |proj g|= 5.35387D+00 + +At iterate 23 f= 2.41885D+06 |proj g|= 4.70172D+00 + +At iterate 24 f= 2.41885D+06 |proj g|= 3.72673D+00 + +At iterate 25 f= 2.41885D+06 |proj g|= 7.03875D-01 + + * * * + +Tit = total number of iterations +Tnf = total number of function evaluations +Tnint = total number of segments explored during Cauchy searches +Skip = number of BFGS updates skipped +Nact = number of active bounds at final generalized Cauchy point +Projg = norm of the final projected gradient +F = final function value + + * * * + + N Tit Tnf Tnint Skip Nact Projg F + 8 25 29 32 0 1 7.039D-01 2.419D+06 + F = 2418846.2058528652 + +CONVERGENCE: REL_REDUCTION_OF_F_<=_FACTR*EPSMCH + + Cauchy time 0.000E+00 seconds. + Subspace minimization time 0.000E+00 seconds. + Line search time 0.000E+00 seconds. + + Total User time 0.000E+00 seconds. + diff --git a/estimates/smcpp_converged/a2/BOT_X100_20K/K1/g0/n32/smcpp/plot.csv b/estimates/smcpp_converged/a2/BOT_X100_20K/K1/g0/n32/smcpp/plot.csv new file mode 100644 index 0000000000000000000000000000000000000000..ffd819c1e6d90120dd37ba0bda3e969f3b291a0c --- 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+pop1,15808.668391515906,2222.082393520187,path,0 +pop1,16259.689111618167,2222.082393520187,path,0 +pop1,16723.577436057734,2222.082393520187,path,0 +pop1,17200.700477106835,1576.1269650040842,path,0 diff --git a/estimates/smcpp_converged/a2/BOT_X100_20K/K1/g0/n32/smcpp/plot.err b/estimates/smcpp_converged/a2/BOT_X100_20K/K1/g0/n32/smcpp/plot.err new file mode 100644 index 0000000000000000000000000000000000000000..f881a10e4f1bcb62d6e3768deaff336eba45dcae --- /dev/null +++ b/estimates/smcpp_converged/a2/BOT_X100_20K/K1/g0/n32/smcpp/plot.err @@ -0,0 +1,2 @@ +/ibex/sw/csi/smcpp/1.15.2/linux_binary/smcpp/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. + from ._conv import register_converters as _register_converters diff --git a/estimates/smcpp_converged/a2/BOT_X100_20K/K1/g0/n32/smcpp/vcf2smc.err b/estimates/smcpp_converged/a2/BOT_X100_20K/K1/g0/n32/smcpp/vcf2smc.err new file mode 100644 index 0000000000000000000000000000000000000000..d21d2320fd3e7ffea1cad06d8991f009c00f8da5 --- /dev/null +++ b/estimates/smcpp_converged/a2/BOT_X100_20K/K1/g0/n32/smcpp/vcf2smc.err @@ -0,0 +1,32 @@ +/ibex/sw/csi/smcpp/1.15.2/linux_binary/smcpp/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. + from ._conv import register_converters as _register_converters +478 smcpp.commands.vcf2smc WARNING Neither missing cutoff (-c) or mask (-m) has been specified. This means that stretches of the chromosome that do not have any VCF entries (for example, centromeres) will be interpreted as homozygous recessive. +478 smcpp.commands.vcf2smc INFO Population 1: +478 smcpp.commands.vcf2smc INFO Distinguished lineages: sample0:0, sample0:1 +478 smcpp.commands.vcf2smc INFO Undistinguished lineages: sample1:0, sample1:1, sample2:0, sample2:1, sample3:0, sample3:1, sample4:0, sample4:1, sample5:0, sample5:1, sample6:0, sample6:1, sample7:0, sample7:1, sample8:0, sample8:1, sample9:0, sample9:1, sample10:0, sample10:1, sample11:0, sample11:1, sample12:0, sample12:1, sample13:0, sample13:1, sample14:0, sample14:1, sample15:0, sample15:1, sample16:0, sample16:1, sample17:0, sample17:1, sample18:0, sample18:1, sample19:0, sample19:1, sample20:0, sample20:1, sample21:0, sample21:1, sample22:0, sample22:1, sample23:0, sample23:1, sample24:0, sample24:1, sample25:0, sample25:1, sample26:0, sample26:1, sample27:0, sample27:1, sample28:0, sample28:1, sample29:0, sample29:1, sample30:0, sample30:1, sample31:0, sample31:1 + 0%| | 0.00/30.0M [00:00 0 & seen; non-finite -> 0; < 500 variants -> absent; cache order; join on canonical_id", + "store_rows": 12, + "store_rows_not_in_cache": 1, + "store_shards": [ + [ + "psmcplus_00000.npz", + "ca392523e02bc3db1011fe3e2d209718637a42f1214f50b69a0fb81f139bfd18" + ] + ], + "utc": "2026-09-16T17:40:01Z", + "width": 256 +} \ No newline at end of file diff --git a/necast_inputs/a2/Africa_1T12/registry/DONE.json b/necast_inputs/a2/Africa_1T12/registry/DONE.json new file mode 100644 index 0000000000000000000000000000000000000000..7291f0438e00e74cd60cb1e9db7b7c87f21445ce --- /dev/null +++ b/necast_inputs/a2/Africa_1T12/registry/DONE.json @@ -0,0 +1,9 @@ +{ + "all_raw_roundtrips_passed": true, + "raw_index_sha256": "ca46feb6255d211f34e53c372c0918494d3d8ffd5d1653aac3eba901ffe33960", + "report_sha256": "e7955ca32b9477c1526ae3058499a2ff1d986f898656f0221e4f1e4146e55689", + "schema": "dlcoalsim-lossless-raw-site-index-v1", + "schema_version": 1, + "selected_samples": 11, + "status": "complete" +} diff --git a/necast_inputs/a2/Africa_1T12/registry/PLAN.json b/necast_inputs/a2/Africa_1T12/registry/PLAN.json new file mode 100644 index 0000000000000000000000000000000000000000..862ca21c79e9a2362367ebce708bcc07e204153e --- /dev/null +++ b/necast_inputs/a2/Africa_1T12/registry/PLAN.json @@ -0,0 +1,67 @@ +{ + "architecture_split_sha256": "1769d06fdb33e0728374a2e15d56cd0f59062e6cec8c5551349d45d37be7a2c6", + "builder_deployment": null, + "command": [ + "/ibex/project/c2041/hany0c/deploy_20260913_fixed32/training/raw_site_gate.py", + "--snapshot", + "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/v2_a2_Africa_1T12/freeze/snapshot.json", + "--reference-cache", + "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/v2_a2_Africa_1T12/freeze/reference_cache.npz", + "--identities", + "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/v2_a2_Africa_1T12/freeze/sample_identities.jsonl", + "--architecture-split", + "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/v2_a2_Africa_1T12/freeze/architecture_split.jsonl", + "--out-dir", + "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/v2_a2_Africa_1T12/registry", + "--gate-samples", + "11", + "--source-root-map", + "/ibex/project/c2041/hany0c/bench_h2h_20260915/data/v2_a2_Africa_1T12=/ibex/project/c2041/hany0c/bench_h2h_20260915/data/.mirrors/v2_a2_Africa_1T12" + ], + "identities_sha256": "57de26755f349e37d7a1ff3c222653639771a9e90bad7055b4d1a34b35102f87", + "observation_schema": "uint32-position-uint8-packed128-sparse-missing-exact-v1", + "physical_source_root_map": { + "/ibex/project/c2041/hany0c/bench_h2h_20260915/data/v2_a2_Africa_1T12": "/ibex/project/c2041/hany0c/bench_h2h_20260915/data/.mirrors/v2_a2_Africa_1T12" + }, + "reference_cache": 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"implemented": false, + "reason": "the existing 19-channel irregular-site Fourier moment map is non-injective and has no unique binary/missing-aware inverse; an arbitrary pseudoinverse would be a fabricated scientific mechanism" + }, + "losslessness_scope": "input/storage only; the learned 100 bp-to-1 Mb latent pyramid is deliberately not invertible", + "missing_policy": "packed simulator bits are retained for byte audit but a downstream model must erase alleles at missing calls", + "representation": "index-only exact persisted raw positions, packed 64-haplotype calls and sparse missing calls", + "targets": "direct 64 log10-Ne bins only" + }, + "selected_samples": 11, + "selection_excluded_before_raw_task_construction": true, + "selection_rows_excluded_before_variant_count_access": 1, + "snapshot": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/v2_a2_Africa_1T12/freeze/snapshot.json", + "snapshot_sha256": "231ab3589c34071a8545d17b07ff885bdc1b4b2652555a460290f653c0385aa4", + "status": "indexing", + "verify_source_sha256": true +} diff --git a/necast_inputs/a2/Africa_1T12/registry/architecture_split.jsonl b/necast_inputs/a2/Africa_1T12/registry/architecture_split.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..ac5b6fb3cb35140c688667ec962db2e4a142d18e --- /dev/null +++ b/necast_inputs/a2/Africa_1T12/registry/architecture_split.jsonl @@ -0,0 +1,11 @@ +{"architecture_group": "bench:30c4e49a7d167e610fb159353a709e196069b1bfe37d025a0a2846530d250661:00000000", "canonical_id": "30c4e49a7d167e610fb159353a709e196069b1bfe37d025a0a2846530d250661:00000000", "seed": 2066200002, "split": "validation"} +{"architecture_group": "bench:30c4e49a7d167e610fb159353a709e196069b1bfe37d025a0a2846530d250661:00000001", "canonical_id": "30c4e49a7d167e610fb159353a709e196069b1bfe37d025a0a2846530d250661:00000001", "seed": 2066207921, "split": "validation"} +{"architecture_group": "bench:30c4e49a7d167e610fb159353a709e196069b1bfe37d025a0a2846530d250661:00000002", "canonical_id": "30c4e49a7d167e610fb159353a709e196069b1bfe37d025a0a2846530d250661:00000002", "seed": 2066215840, "split": "validation"} +{"architecture_group": "bench:30c4e49a7d167e610fb159353a709e196069b1bfe37d025a0a2846530d250661:00000003", "canonical_id": "30c4e49a7d167e610fb159353a709e196069b1bfe37d025a0a2846530d250661:00000003", "seed": 2066223759, "split": "validation"} +{"architecture_group": "bench:30c4e49a7d167e610fb159353a709e196069b1bfe37d025a0a2846530d250661:00000004", "canonical_id": "30c4e49a7d167e610fb159353a709e196069b1bfe37d025a0a2846530d250661:00000004", "seed": 2066231678, "split": "validation"} +{"architecture_group": "bench:30c4e49a7d167e610fb159353a709e196069b1bfe37d025a0a2846530d250661:00000005", "canonical_id": "30c4e49a7d167e610fb159353a709e196069b1bfe37d025a0a2846530d250661:00000005", "seed": 2066239597, "split": "validation"} +{"architecture_group": "bench:30c4e49a7d167e610fb159353a709e196069b1bfe37d025a0a2846530d250661:00000006", "canonical_id": 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smallest/largest exact variant count; canonical_id tie break; publish reference row order", + "variant_count_max": 110251, + "variant_count_min": 95342 +} diff --git a/necast_inputs/a2/Africa_1T12/registry/raw_index.jsonl b/necast_inputs/a2/Africa_1T12/registry/raw_index.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..59d5cf424869fdd7fbab9d9b6b70c78f8a1a7433 --- /dev/null +++ b/necast_inputs/a2/Africa_1T12/registry/raw_index.jsonl @@ -0,0 +1,11 @@ +{"canonical_id": "30c4e49a7d167e610fb159353a709e196069b1bfe37d025a0a2846530d250661:00000000", "logical_dataset_root": "/ibex/project/c2041/hany0c/bench_h2h_20260915/data/v2_a2_Africa_1T12", "missing_call_count": 213776, "offsets": {"missing": [0, 213776], "obs_mut_pos": [0, 2], "obs_mut_rate": [0, 1], "obs_rec_pos": [0, 2], "obs_rec_rate": [0, 1], "variant": [0, 98164]}, "output_index": 0, "physical_dataset_root": "/ibex/project/c2041/hany0c/bench_h2h_20260915/data/.mirrors/v2_a2_Africa_1T12", 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