== compiling C++ simulator and MSA aligner == == running experiment == === pi_long=0.00 : generating dev/test data === [simulate] /work/src/simulate 100 0.0 4 6 220 /work/data/pi0.00_dev_seed100 :: simulate: seed=100 pi_long=0.00 n_families=4 n_taxa=6 root_len=220 -> /work/data/pi0.00_dev_seed100_fam*.fa [simulate] /work/src/simulate 101 0.0 4 6 220 /work/data/pi0.00_dev_seed101 :: simulate: seed=101 pi_long=0.00 n_families=4 n_taxa=6 root_len=220 -> /work/data/pi0.00_dev_seed101_fam*.fa [simulate] /work/src/simulate 102 0.0 4 6 220 /work/data/pi0.00_dev_seed102 :: simulate: seed=102 pi_long=0.00 n_families=4 n_taxa=6 root_len=220 -> /work/data/pi0.00_dev_seed102_fam*.fa [simulate] /work/src/simulate 0 0.0 4 6 220 /work/data/pi0.00_test_seed0 :: simulate: seed=0 pi_long=0.00 n_families=4 n_taxa=6 root_len=220 -> /work/data/pi0.00_test_seed0_fam*.fa [simulate] /work/src/simulate 1 0.0 4 6 220 /work/data/pi0.00_test_seed1 :: simulate: seed=1 pi_long=0.00 n_families=4 n_taxa=6 root_len=220 -> /work/data/pi0.00_test_seed1_fam*.fa [simulate] /work/src/simulate 2 0.0 4 6 220 /work/data/pi0.00_test_seed2 :: simulate: seed=2 pi_long=0.00 n_families=4 n_taxa=6 root_len=220 -> /work/data/pi0.00_test_seed2_fam*.fa [grid] baseline 1-piece: 20 combos x 12 dev families [grid] best baseline (O,E)=(4, 3) dev_sp=0.3561 [grid] proposed 2-piece: 20 combos x 12 dev families (O1=4,E1=3 fixed) [grid] best proposed (O2,E2)=(28, 0.4) dev_sp=0.3544 === pi_long=0.05 : generating dev/test data === [simulate] /work/src/simulate 100 0.05 4 6 220 /work/data/pi0.05_dev_seed100 :: simulate: seed=100 pi_long=0.05 n_families=4 n_taxa=6 root_len=220 -> /work/data/pi0.05_dev_seed100_fam*.fa [simulate] /work/src/simulate 101 0.05 4 6 220 /work/data/pi0.05_dev_seed101 :: simulate: seed=101 pi_long=0.05 n_families=4 n_taxa=6 root_len=220 -> /work/data/pi0.05_dev_seed101_fam*.fa [simulate] /work/src/simulate 102 0.05 4 6 220 /work/data/pi0.05_dev_seed102 :: simulate: seed=102 pi_long=0.05 n_families=4 n_taxa=6 root_len=220 -> /work/data/pi0.05_dev_seed102_fam*.fa [simulate] /work/src/simulate 0 0.05 4 6 220 /work/data/pi0.05_test_seed0 :: simulate: seed=0 pi_long=0.05 n_families=4 n_taxa=6 root_len=220 -> /work/data/pi0.05_test_seed0_fam*.fa [simulate] /work/src/simulate 1 0.05 4 6 220 /work/data/pi0.05_test_seed1 :: simulate: seed=1 pi_long=0.05 n_families=4 n_taxa=6 root_len=220 -> /work/data/pi0.05_test_seed1_fam*.fa [simulate] /work/src/simulate 2 0.05 4 6 220 /work/data/pi0.05_test_seed2 :: simulate: seed=2 pi_long=0.05 n_families=4 n_taxa=6 root_len=220 -> /work/data/pi0.05_test_seed2_fam*.fa [grid] baseline 1-piece: 20 combos x 12 dev families [grid] best baseline (O,E)=(4, 3) dev_sp=0.3548 [grid] proposed 2-piece: 20 combos x 12 dev families (O1=4,E1=3 fixed) [grid] best proposed (O2,E2)=(24, 0.4) dev_sp=0.3565 === pi_long=0.20 : generating dev/test data === [simulate] /work/src/simulate 100 0.2 4 6 220 /work/data/pi0.20_dev_seed100 :: simulate: seed=100 pi_long=0.20 n_families=4 n_taxa=6 root_len=220 -> /work/data/pi0.20_dev_seed100_fam*.fa [simulate] /work/src/simulate 101 0.2 4 6 220 /work/data/pi0.20_dev_seed101 :: simulate: seed=101 pi_long=0.20 n_families=4 n_taxa=6 root_len=220 -> /work/data/pi0.20_dev_seed101_fam*.fa [simulate] /work/src/simulate 102 0.2 4 6 220 /work/data/pi0.20_dev_seed102 :: simulate: seed=102 pi_long=0.20 n_families=4 n_taxa=6 root_len=220 -> /work/data/pi0.20_dev_seed102_fam*.fa [simulate] /work/src/simulate 0 0.2 4 6 220 /work/data/pi0.20_test_seed0 :: simulate: seed=0 pi_long=0.20 n_families=4 n_taxa=6 root_len=220 -> /work/data/pi0.20_test_seed0_fam*.fa [simulate] /work/src/simulate 1 0.2 4 6 220 /work/data/pi0.20_test_seed1 :: simulate: seed=1 pi_long=0.20 n_families=4 n_taxa=6 root_len=220 -> /work/data/pi0.20_test_seed1_fam*.fa [simulate] /work/src/simulate 2 0.2 4 6 220 /work/data/pi0.20_test_seed2 :: simulate: seed=2 pi_long=0.20 n_families=4 n_taxa=6 root_len=220 -> /work/data/pi0.20_test_seed2_fam*.fa [grid] baseline 1-piece: 20 combos x 12 dev families [grid] best baseline (O,E)=(4, 3) dev_sp=0.2741 [grid] proposed 2-piece: 20 combos x 12 dev families (O1=4,E1=3 fixed) [grid] best proposed (O2,E2)=(16, 0.4) dev_sp=0.2838 pi=0.00 baseline grid O=4 E=0.5 dev_mean_sp=0.3085 pi=0.00 baseline grid O=4 E=1 dev_mean_sp=0.3162 pi=0.00 baseline grid O=4 E=2 dev_mean_sp=0.3501 pi=0.00 baseline grid O=4 E=3 dev_mean_sp=0.3561 pi=0.00 baseline grid O=6 E=0.5 dev_mean_sp=0.3113 pi=0.00 baseline grid O=6 E=1 dev_mean_sp=0.3135 pi=0.00 baseline grid O=6 E=2 dev_mean_sp=0.3402 pi=0.00 baseline grid O=6 E=3 dev_mean_sp=0.3479 pi=0.00 baseline grid O=8 E=0.5 dev_mean_sp=0.3284 pi=0.00 baseline grid O=8 E=1 dev_mean_sp=0.3269 pi=0.00 baseline grid O=8 E=2 dev_mean_sp=0.3406 pi=0.00 baseline grid O=8 E=3 dev_mean_sp=0.3394 pi=0.00 baseline grid O=10 E=0.5 dev_mean_sp=0.3315 pi=0.00 baseline grid O=10 E=1 dev_mean_sp=0.3275 pi=0.00 baseline grid O=10 E=2 dev_mean_sp=0.3395 pi=0.00 baseline grid O=10 E=3 dev_mean_sp=0.3395 pi=0.00 baseline grid O=12 E=0.5 dev_mean_sp=0.3269 pi=0.00 baseline grid O=12 E=1 dev_mean_sp=0.3278 pi=0.00 baseline grid O=12 E=2 dev_mean_sp=0.3385 pi=0.00 baseline grid O=12 E=3 dev_mean_sp=0.3390 pi=0.00 proposed grid O2=12 E2=0.05 dev_mean_sp=0.3341 pi=0.00 proposed grid O2=12 E2=0.1 dev_mean_sp=0.3338 pi=0.00 proposed grid O2=12 E2=0.2 dev_mean_sp=0.3466 pi=0.00 proposed grid O2=12 E2=0.4 dev_mean_sp=0.3498 pi=0.00 proposed grid O2=16 E2=0.05 dev_mean_sp=0.3352 pi=0.00 proposed grid O2=16 E2=0.1 dev_mean_sp=0.3468 pi=0.00 proposed grid O2=16 E2=0.2 dev_mean_sp=0.3475 pi=0.00 proposed grid O2=16 E2=0.4 dev_mean_sp=0.3520 pi=0.00 proposed grid O2=20 E2=0.05 dev_mean_sp=0.3466 pi=0.00 proposed grid O2=20 E2=0.1 dev_mean_sp=0.3489 pi=0.00 proposed grid O2=20 E2=0.2 dev_mean_sp=0.3464 pi=0.00 proposed grid O2=20 E2=0.4 dev_mean_sp=0.3524 pi=0.00 proposed grid O2=24 E2=0.05 dev_mean_sp=0.3463 pi=0.00 proposed grid O2=24 E2=0.1 dev_mean_sp=0.3490 pi=0.00 proposed grid O2=24 E2=0.2 dev_mean_sp=0.3457 pi=0.00 proposed grid O2=24 E2=0.4 dev_mean_sp=0.3525 pi=0.00 proposed grid O2=28 E2=0.05 dev_mean_sp=0.3461 pi=0.00 proposed grid O2=28 E2=0.1 dev_mean_sp=0.3468 pi=0.00 proposed grid O2=28 E2=0.2 dev_mean_sp=0.3456 pi=0.00 proposed grid O2=28 E2=0.4 dev_mean_sp=0.3544 pi=0.00 seed=0 baseline: no true gap>=10 in any of 4 test families -> sp_near_long_indel falls back to sp_score=0.4505 pi=0.00 seed=0 proposed: no true gap>=10 in any of 4 test families -> sp_near_long_indel falls back to sp_score=0.4475 pi=0.00 seed=0 baseline sp=0.4505 proposed sp=0.4475 pi=0.00 seed=1 baseline: no true gap>=10 in any of 4 test families -> sp_near_long_indel falls back to sp_score=0.4779 pi=0.00 seed=1 proposed: no true gap>=10 in any of 4 test families -> sp_near_long_indel falls back to sp_score=0.4838 pi=0.00 seed=1 baseline sp=0.4779 proposed sp=0.4838 pi=0.00 seed=2 baseline: no true gap>=10 in any of 4 test families -> sp_near_long_indel falls back to sp_score=0.5207 pi=0.00 seed=2 proposed: no true gap>=10 in any of 4 test families -> sp_near_long_indel falls back to sp_score=0.5207 pi=0.00 seed=2 baseline sp=0.5207 proposed sp=0.5207 pi=0.05 baseline grid O=4 E=0.5 dev_mean_sp=0.3125 pi=0.05 baseline grid O=4 E=1 dev_mean_sp=0.3213 pi=0.05 baseline grid O=4 E=2 dev_mean_sp=0.3520 pi=0.05 baseline grid O=4 E=3 dev_mean_sp=0.3548 pi=0.05 baseline grid O=6 E=0.5 dev_mean_sp=0.3163 pi=0.05 baseline grid O=6 E=1 dev_mean_sp=0.3183 pi=0.05 baseline grid O=6 E=2 dev_mean_sp=0.3433 pi=0.05 baseline grid O=6 E=3 dev_mean_sp=0.3498 pi=0.05 baseline grid O=8 E=0.5 dev_mean_sp=0.3348 pi=0.05 baseline grid O=8 E=1 dev_mean_sp=0.3323 pi=0.05 baseline grid O=8 E=2 dev_mean_sp=0.3444 pi=0.05 baseline grid O=8 E=3 dev_mean_sp=0.3434 pi=0.05 baseline grid O=10 E=0.5 dev_mean_sp=0.3366 pi=0.05 baseline grid O=10 E=1 dev_mean_sp=0.3325 pi=0.05 baseline grid O=10 E=2 dev_mean_sp=0.3441 pi=0.05 baseline grid O=10 E=3 dev_mean_sp=0.3434 pi=0.05 baseline grid O=12 E=0.5 dev_mean_sp=0.3323 pi=0.05 baseline grid O=12 E=1 dev_mean_sp=0.3327 pi=0.05 baseline grid O=12 E=2 dev_mean_sp=0.3424 pi=0.05 baseline grid O=12 E=3 dev_mean_sp=0.3429 pi=0.05 proposed grid O2=12 E2=0.05 dev_mean_sp=0.3398 pi=0.05 proposed grid O2=12 E2=0.1 dev_mean_sp=0.3397 pi=0.05 proposed grid O2=12 E2=0.2 dev_mean_sp=0.3517 pi=0.05 proposed grid O2=12 E2=0.4 dev_mean_sp=0.3558 pi=0.05 proposed grid O2=16 E2=0.05 dev_mean_sp=0.3409 pi=0.05 proposed grid O2=16 E2=0.1 dev_mean_sp=0.3523 pi=0.05 proposed grid O2=16 E2=0.2 dev_mean_sp=0.3533 pi=0.05 proposed grid O2=16 E2=0.4 dev_mean_sp=0.3556 pi=0.05 proposed grid O2=20 E2=0.05 dev_mean_sp=0.3519 pi=0.05 proposed grid O2=20 E2=0.1 dev_mean_sp=0.3550 pi=0.05 proposed grid O2=20 E2=0.2 dev_mean_sp=0.3529 pi=0.05 proposed grid O2=20 E2=0.4 dev_mean_sp=0.3561 pi=0.05 proposed grid O2=24 E2=0.05 dev_mean_sp=0.3525 pi=0.05 proposed grid O2=24 E2=0.1 dev_mean_sp=0.3551 pi=0.05 proposed grid O2=24 E2=0.2 dev_mean_sp=0.3518 pi=0.05 proposed grid O2=24 E2=0.4 dev_mean_sp=0.3565 pi=0.05 proposed grid O2=28 E2=0.05 dev_mean_sp=0.3525 pi=0.05 proposed grid O2=28 E2=0.1 dev_mean_sp=0.3528 pi=0.05 proposed grid O2=28 E2=0.2 dev_mean_sp=0.3517 pi=0.05 proposed grid O2=28 E2=0.4 dev_mean_sp=0.3564 pi=0.05 seed=0 baseline sp=0.3438 proposed sp=0.3408 pi=0.05 seed=1 baseline sp=0.4808 proposed sp=0.4984 pi=0.05 seed=2 baseline: no true gap>=10 in any of 4 test families -> sp_near_long_indel falls back to sp_score=0.5207 pi=0.05 seed=2 proposed: no true gap>=10 in any of 4 test families -> sp_near_long_indel falls back to sp_score=0.5207 pi=0.05 seed=2 baseline sp=0.5207 proposed sp=0.5207 pi=0.20 baseline grid O=4 E=0.5 dev_mean_sp=0.2436 pi=0.20 baseline grid O=4 E=1 dev_mean_sp=0.2619 pi=0.20 baseline grid O=4 E=2 dev_mean_sp=0.2691 pi=0.20 baseline grid O=4 E=3 dev_mean_sp=0.2741 pi=0.20 baseline grid O=6 E=0.5 dev_mean_sp=0.2593 pi=0.20 baseline grid O=6 E=1 dev_mean_sp=0.2644 pi=0.20 baseline grid O=6 E=2 dev_mean_sp=0.2628 pi=0.20 baseline grid O=6 E=3 dev_mean_sp=0.2646 pi=0.20 baseline grid O=8 E=0.5 dev_mean_sp=0.2636 pi=0.20 baseline grid O=8 E=1 dev_mean_sp=0.2633 pi=0.20 baseline grid O=8 E=2 dev_mean_sp=0.2620 pi=0.20 baseline grid O=8 E=3 dev_mean_sp=0.2594 pi=0.20 baseline grid O=10 E=0.5 dev_mean_sp=0.2684 pi=0.20 baseline grid O=10 E=1 dev_mean_sp=0.2617 pi=0.20 baseline grid O=10 E=2 dev_mean_sp=0.2633 pi=0.20 baseline grid O=10 E=3 dev_mean_sp=0.2647 pi=0.20 baseline grid O=12 E=0.5 dev_mean_sp=0.2660 pi=0.20 baseline grid O=12 E=1 dev_mean_sp=0.2650 pi=0.20 baseline grid O=12 E=2 dev_mean_sp=0.2645 pi=0.20 baseline grid O=12 E=3 dev_mean_sp=0.2667 pi=0.20 proposed grid O2=12 E2=0.05 dev_mean_sp=0.2780 pi=0.20 proposed grid O2=12 E2=0.1 dev_mean_sp=0.2809 pi=0.20 proposed grid O2=12 E2=0.2 dev_mean_sp=0.2819 pi=0.20 proposed grid O2=12 E2=0.4 dev_mean_sp=0.2825 pi=0.20 proposed grid O2=16 E2=0.05 dev_mean_sp=0.2782 pi=0.20 proposed grid O2=16 E2=0.1 dev_mean_sp=0.2805 pi=0.20 proposed grid O2=16 E2=0.2 dev_mean_sp=0.2809 pi=0.20 proposed grid O2=16 E2=0.4 dev_mean_sp=0.2838 pi=0.20 proposed grid O2=20 E2=0.05 dev_mean_sp=0.2782 pi=0.20 proposed grid O2=20 E2=0.1 dev_mean_sp=0.2814 pi=0.20 proposed grid O2=20 E2=0.2 dev_mean_sp=0.2822 pi=0.20 proposed grid O2=20 E2=0.4 dev_mean_sp=0.2831 pi=0.20 proposed grid O2=24 E2=0.05 dev_mean_sp=0.2773 pi=0.20 proposed grid O2=24 E2=0.1 dev_mean_sp=0.2805 pi=0.20 proposed grid O2=24 E2=0.2 dev_mean_sp=0.2811 pi=0.20 proposed grid O2=24 E2=0.4 dev_mean_sp=0.2819 pi=0.20 proposed grid O2=28 E2=0.05 dev_mean_sp=0.2777 pi=0.20 proposed grid O2=28 E2=0.1 dev_mean_sp=0.2809 pi=0.20 proposed grid O2=28 E2=0.2 dev_mean_sp=0.2797 pi=0.20 proposed grid O2=28 E2=0.4 dev_mean_sp=0.2821 pi=0.20 seed=0 baseline sp=0.3438 proposed sp=0.3406 pi=0.20 seed=1 baseline sp=0.4808 proposed sp=0.4985 pi=0.20 seed=2 baseline sp=0.5561 proposed sp=0.5620 === SUMMARY === pi_long=0.00 baseline_sp=0.4830 proposed_sp=0.4840 gain_pp=0.09 pi_long=0.05 baseline_sp=0.4484 proposed_sp=0.4533 gain_pp=0.49 pi_long=0.20 baseline_sp=0.4602 proposed_sp=0.4670 gain_pp=0.68 prediction_outcome=refuted runtime_sec=20.1 wrote figs/sp_gain_vs_pi_long.png