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0.09999232464815883, + 0.10008575176449812, + 0.15002622329576404, + 0.24994284320006627, + 1.1718203201573796 + ], + "pid": "pop1", + "spline_class": "Piecewise", + "y": [ + 1.3207190000279596, + 1.3139995901031045, + 1.307260785641251, + 1.3037620261950325, + 1.3141010873828627, + 1.3239183976235582, + 1.3277388979221003, + 1.3277590574111944, + 1.3276856221011357, + 1.3264011336590271, + 1.3164645644304314, + 1.2689698331617163, + 1.1620452398859957, + 1.0056784749924879, + 0.8425352087747143, + 0.6735375171546576 + ] + }, + "rho": 7.999999857891455e-05, + "theta": 0.0001 +} \ No newline at end of file diff --git a/estimates/smcpp/a1/BOT_X100_1K/K1/g0/n32/smcpp/estimate.cmd b/estimates/smcpp/a1/BOT_X100_1K/K1/g0/n32/smcpp/estimate.cmd new file mode 100644 index 0000000000000000000000000000000000000000..d2ce32a0af09f9168f980422ee2de8c18b210296 --- /dev/null +++ b/estimates/smcpp/a1/BOT_X100_1K/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/v2_a1_BOT_X100_1K/K1/g0/n32/smcpp/est --unfold -r 9.99999993922529e-09 --regularization-penalty 3.0 1.2500000146076218e-08 /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/smcpp/EQ/tune_d4_rp3/v2_a1_BOT_X100_1K/K1/g0/n32/smcpp/data/region_0.d0.smc.gz /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/smcpp/EQ/tune_d4_rp3/v2_a1_BOT_X100_1K/K1/g0/n32/smcpp/data/region_0.d1.smc.gz /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/smcpp/EQ/tune_d4_rp3/v2_a1_BOT_X100_1K/K1/g0/n32/smcpp/data/region_0.d2.smc.gz /ibex/project/c2041/hany0c/bench_h2h_20260915/fits/v1/smcpp/EQ/tune_d4_rp3/v2_a1_BOT_X100_1K/K1/g0/n32/smcpp/data/region_0.d3.smc.gz diff --git a/estimates/smcpp/a1/BOT_X100_1K/K1/g0/n32/smcpp/estimate.err b/estimates/smcpp/a1/BOT_X100_1K/K1/g0/n32/smcpp/estimate.err new file mode 100644 index 0000000000000000000000000000000000000000..1a4a44b4d32a38fab03fb95f784d20db86a09022 --- /dev/null +++ b/estimates/smcpp/a1/BOT_X100_1K/K1/g0/n32/smcpp/estimate.err @@ -0,0 +1,224 @@ +/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 +872 smcpp.analysis.base INFO theta: 0.000100 +872 smcpp.analysis.base INFO rho: 0.000080 +872 smcpp.analysis.base WARNING Using unfolded SFS. The user should verify that the ancestral allele has been correctly coded. +872 smcpp.data_filter INFO Loading data... +947 smcpp.data_filter INFO 0.12 Gb of data +949 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 +3360 smcpp.optimize.plugins.progress_printer INFO Starting EM algorithm... +3360 smcpp.optimize.plugins.progress_printer INFO EM iteration 1 of 1... +3360 smcpp.analysis.base INFO Running E-step +3431 smcpp.analysis.base INFO E-step completed +3433 smcpp.optimize.plugins.loglikelihood_monitor INFO Loglik: -1003549.260486 +24608 smcpp.optimize.plugins.progress_printer INFO Current model: + + 0.21 -1.08 -1.38 -1.03 -0.38 0.40 1.21 2.02 + 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 1.23 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.25 0.25 0.25 0.25 0.25 0.25 0.25 0.25 0.25 0.25 0.25 0.25 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.69 0.69 0.69 0.69 0.69 0.69 0.69 0.69 1.49 1.49 1.49 1.49 1.49 1.49 1.49 1.49 1.49 1.49 3.36 3.36 3.36 3.36 3.36 3.36 3.36 3.36 3.36 3.36 7.53 +24628 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 100000 +++-+-+-----------+-------+----+---+--+--+--+-+-+-----------+--+++ + ++ + + ++ + ++ Pop. 1 *******++ + ++ ++ + ++ +B + ++ +* + | B******| + 10000 +++ * +++ + ++ * ++ + B********************* B****** ++ + ++ * * ++ + ++ * B***** ++ + ++ * * ++ + | + B*********** B****** + | + 1000 +-+-+-+-----------+-------+----+B*******-+--+-+-+-----------+--+-+ + 1000 10000 + Generations + + +24631 smcpp.data_filter INFO Loading data... +24771 smcpp.data_filter INFO 0.12 Gb of data +24773 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 +29216 smcpp.optimize.plugins.progress_printer INFO Starting EM algorithm... +29216 smcpp.optimize.plugins.progress_printer INFO EM iteration 1 of 20... +29216 smcpp.analysis.base INFO Running E-step +31045 smcpp.analysis.base INFO E-step completed +31049 smcpp.optimize.plugins.loglikelihood_monitor INFO Loglik: -53015.561270 +152204 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 100000 +++----+--++---+-----+-+-+---+----+--++---+-----+--++---+----+-+++ + ++ + + + + ++ + ++ Pop. 1 *******++ + ++ ++ + ++ ++ + ++ ++ + B*B*B**B**************************************B****B*B*** | + 10000 +++ B********+ + ++ +* + ++ +B + ++ ++ + ++ ++ + ++ ++ + | + + + + | + 1000 +-+----+--++---+-----+-+-+---+----+--++---+-----+--++---+----+-+-+ + 1 10 100 1000 + Generations + + +152205 smcpp.optimize.plugins.progress_printer INFO Current model: + + 1.21 1.20 1.20 1.20 1.21 1.21 1.21 1.21 1.21 1.21 1.21 1.21 1.18 1.09 0.84 0.32 + 3.34 3.34 3.34 3.33 3.33 3.33 3.33 3.33 3.33 3.33 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.32 3.34 3.34 3.34 3.34 3.34 3.34 3.25 3.25 3.25 3.25 2.96 2.96 2.96 2.96 2.96 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 1.38 +152206 smcpp.optimize.plugins.progress_printer INFO EM iteration 2 of 20... +152206 smcpp.analysis.base INFO Running E-step +154494 smcpp.analysis.base INFO E-step completed +154498 smcpp.optimize.plugins.loglikelihood_monitor INFO New loglik: -52863.960708 (old: -53015.561270 [0.285955%]) +276269 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 100000 +++----+--++---+-----+-+-+---+----+--++---+-----+--++---+----+-+++ + ++ + + + + ++ + ++ Pop. 1 *******++ + ++ ++ + ++ ++ + B*B*B**B**************************************B****B ++ + | B*B*** | + 10000 +++ B********+ + ++ +B + ++ ++ + ++ ++ + ++ ++ + ++ ++ + | + + + + | + 1000 +-+----+--++---+-----+-+-+---+----+--++---+-----+--++---+----+-+-+ + 1 10 100 1000 + Generations + + +276270 smcpp.optimize.plugins.progress_printer INFO Current model: + + 1.47 1.47 1.46 1.46 1.47 1.47 1.47 1.47 1.47 1.47 1.48 1.47 1.41 1.26 1.00 0.57 + 4.35 4.35 4.35 4.33 4.33 4.33 4.33 4.32 4.32 4.32 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.31 4.36 4.36 4.36 4.36 4.36 4.36 4.08 4.08 4.08 4.08 3.54 3.54 3.54 3.54 3.54 2.71 2.71 2.71 2.71 2.71 2.71 2.71 2.71 2.71 2.71 2.71 2.71 2.71 1.76 +276271 smcpp.optimize.plugins.progress_printer INFO EM iteration 3 of 20... +276271 smcpp.analysis.base INFO Running E-step +278563 smcpp.analysis.base INFO E-step completed +278577 smcpp.optimize.plugins.loglikelihood_monitor INFO New loglik: -52846.619008 (old: -52863.960708 [0.032804%]) +400929 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 100000 +++----+--++---+-----+-+-+---+----+--++---+-----+--++---+----+-+++ + ++ + + + + ++ + ++ Pop. 1 *******++ + ++ ++ + ++ ++ + B*B*B**B**************************************B****B ++ + | B*B*** | + 10000 +++ B********+ + ++ +B + ++ ++ + ++ ++ + ++ ++ + ++ ++ + | + + + + | + 1000 +-+----+--++---+-----+-+-+---+----+--++---+-----+--++---+----+-+-+ + 1 10 100 1000 + Generations + + +400930 smcpp.optimize.plugins.progress_printer INFO Current model: + + 1.47 1.46 1.46 1.46 1.47 1.47 1.47 1.47 1.47 1.47 1.48 1.45 1.37 1.21 0.97 0.64 + 4.35 4.35 4.35 4.33 4.33 4.33 4.33 4.30 4.30 4.30 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.29 4.37 4.37 4.37 4.37 4.37 4.37 3.94 3.94 3.94 3.94 3.35 3.35 3.35 3.35 3.35 2.63 2.63 2.63 2.63 2.63 2.63 2.63 2.63 2.63 2.63 2.63 2.63 2.63 1.90 +400931 smcpp.optimize.plugins.progress_printer INFO EM iteration 4 of 20... +400931 smcpp.analysis.base INFO Running E-step +403219 smcpp.analysis.base INFO E-step completed +403223 smcpp.optimize.plugins.loglikelihood_monitor INFO New loglik: -52840.320420 (old: -52846.619008 [0.011919%]) +525868 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 100000 +++----+--++---+-----+-+-+---+----+--++---+-----+--++---+----+-+++ + ++ + + + + ++ + ++ Pop. 1 *******++ + ++ ++ + ++ ++ + ++ ++ + B*B*B**B**************************************B****B*B*** | + 10000 +++ B********+ + ++ +B + ++ ++ + ++ ++ + ++ ++ + ++ ++ + | + + + + | + 1000 +-+----+--++---+-----+-+-+---+----+--++---+-----+--++---+----+-+-+ + 1 10 100 1000 + Generations + + +525869 smcpp.optimize.plugins.progress_printer INFO Current model: + + 1.40 1.39 1.39 1.38 1.39 1.40 1.40 1.40 1.40 1.41 1.40 1.37 1.27 1.11 0.90 0.67 + 4.06 4.06 4.06 4.03 4.03 4.03 4.03 4.01 4.01 4.01 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 3.99 4.08 4.08 4.08 4.08 4.08 4.08 3.56 3.56 3.56 3.56 3.02 3.02 3.02 3.02 3.02 2.47 2.47 2.47 2.47 2.47 2.47 2.47 2.47 2.47 2.47 2.47 2.47 2.47 1.95 +525870 smcpp.optimize.plugins.progress_printer INFO EM iteration 5 of 20... +525871 smcpp.analysis.base INFO Running E-step +528163 smcpp.analysis.base INFO E-step completed +528169 smcpp.optimize.plugins.loglikelihood_monitor INFO New loglik: -52834.930753 (old: -52840.320420 [0.010200%]) +649331 smcpp.optimize.plugins.ascii_plotter INFO Plot of current model: + + + 100000 +++----+--++---+-----+-+-+---+----+--++---+-----+--++---+----+-+++ + ++ + + + + ++ + ++ Pop. 1 *******++ + ++ ++ + ++ ++ + ++ ++ + B*B*B**B**************************************B****B** | + 10000 +++ B**B********+ + ++ +B + ++ ++ + ++ ++ + ++ ++ + ++ ++ + | + + + + | + 1000 +-+----+--++---+-----+-+-+---+----+--++---+-----+--++---+----+-+-+ + 1 10 100 1000 + Generations + + +649332 smcpp.optimize.plugins.progress_printer INFO Current model: + + 1.32 1.31 1.31 1.30 1.31 1.32 1.33 1.33 1.33 1.33 1.32 1.27 1.16 1.01 0.84 0.67 + 3.75 3.75 3.75 3.72 3.72 3.72 3.72 3.70 3.70 3.70 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.68 3.77 3.77 3.77 3.77 3.77 3.77 3.20 3.20 3.20 3.20 2.73 2.73 2.73 2.73 2.73 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 1.96 +649333 smcpp.optimize.plugins.progress_printer INFO EM iteration 6 of 20... +649334 smcpp.analysis.base INFO Running E-step +651624 smcpp.analysis.base INFO E-step completed +651631 smcpp.optimize.plugins.loglikelihood_monitor INFO New loglik: -52830.547131 (old: -52834.930753 [0.008297%]) +651631 smcpp.optimize.plugins.loglikelihood_monitor INFO Log-likelihood improvement < tol=0.0001; terminating diff --git a/estimates/smcpp/a1/BOT_X100_1K/K1/g0/n32/smcpp/estimate.out b/estimates/smcpp/a1/BOT_X100_1K/K1/g0/n32/smcpp/estimate.out new file mode 100644 index 0000000000000000000000000000000000000000..855ba7ae338de96d6c03b211a9aa0a77f2bd330f --- /dev/null +++ b/estimates/smcpp/a1/BOT_X100_1K/K1/g0/n32/smcpp/estimate.out @@ -0,0 +1,79 @@ +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= 9.93885D+05 |proj g|= 3.00000D+00 + +At iterate 1 f= 9.77488D+05 |proj g|= 3.66824D+00 + +At iterate 2 f= 9.74456D+05 |proj g|= 3.49960D+00 + +At iterate 3 f= 9.73341D+05 |proj g|= 4.23313D+00 + +At iterate 4 f= 9.72989D+05 |proj g|= 4.15582D+00 + +At iterate 5 f= 9.72944D+05 |proj g|= 4.14649D+00 + +At iterate 6 f= 9.72904D+05 |proj g|= 4.14718D+00 + +At iterate 7 f= 9.72799D+05 |proj g|= 3.77850D+00 + +At iterate 8 f= 9.72713D+05 |proj g|= 3.99287D+00 + +At iterate 9 f= 9.72637D+05 |proj g|= 4.19743D+00 + +At iterate 10 f= 9.72560D+05 |proj g|= 4.32666D+00 + +At iterate 11 f= 9.72397D+05 |proj g|= 4.70339D+00 + +At iterate 12 f= 9.72190D+05 |proj g|= 4.79683D+00 + +At iterate 13 f= 9.72128D+05 |proj g|= 4.98056D+00 + +At iterate 14 f= 9.72127D+05 |proj g|= 4.99245D+00 + Positive dir derivative in projection + Using the backtracking step + +At iterate 15 f= 9.71879D+05 |proj g|= 5.25514D+00 + +At iterate 16 f= 9.71806D+05 |proj g|= 4.32949D+00 + +At iterate 17 f= 9.71791D+05 |proj g|= 4.36836D+00 + +At iterate 18 f= 9.71790D+05 |proj g|= 4.38792D+00 + +At iterate 19 f= 9.71789D+05 |proj g|= 4.83591D+00 + +At iterate 20 f= 9.71789D+05 |proj g|= 2.83274D+00 + +At iterate 21 f= 9.71789D+05 |proj g|= 8.92098D-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 21 26 28 0 1 8.921D-01 9.718D+05 + F = 971789.22653234226 + +CONVERGENCE: REL_REDUCTION_OF_F_<=_FACTR*EPSMCH + + Cauchy time 0.000E+00 seconds. + Subspace 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b/estimates/smcpp/a1/BOT_X100_1K/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/a1/BOT_X100_1K/K1/g0/n32/smcpp/vcf2smc.err b/estimates/smcpp/a1/BOT_X100_1K/K1/g0/n32/smcpp/vcf2smc.err new file mode 100644 index 0000000000000000000000000000000000000000..fb88061501f3b976af984dd82ef8cfd358925691 --- /dev/null +++ b/estimates/smcpp/a1/BOT_X100_1K/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 +858 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. +858 smcpp.commands.vcf2smc INFO Population 1: +858 smcpp.commands.vcf2smc INFO Distinguished lineages: sample0:0, sample0:1 +858 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