RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 02-Jul-2021 09:42:45 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08575/2_msa/P08575_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08575/3_mltree/P08575 --seed 2 --threads 7 --tree rand{20} pars{20} Analysis options: run mode: ML tree search start tree(s): random (20) random seed: 2 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON fast spr radius: AUTO spr subtree cutoff: 1.000000 branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (7 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08575/2_msa/P08575_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 541 sites WARNING: Sequences tr_B4QA19_B4QA19_DROSI_7240 and sp_P16621_LAR_DROME_7227 are exactly identical! WARNING: Sequences tr_A0A1D5PHX3_A0A1D5PHX3_CHICK_9031 and tr_G1NAN6_G1NAN6_MELGA_9103 are exactly identical! WARNING: Sequences tr_A0A1L1RRB0_A0A1L1RRB0_CHICK_9031 and tr_A0A226P8S9_A0A226P8S9_COLVI_9014 are exactly identical! WARNING: Sequences sp_Q64487_PTPRD_MOUSE_10090 and tr_M0RB22_M0RB22_RAT_10116 are exactly identical! WARNING: Sequences sp_Q99M80_PTPRT_MOUSE_10090 and tr_H0XB99_H0XB99_OTOGA_30611 are exactly identical! WARNING: Sequences sp_Q99M80_PTPRT_MOUSE_10090 and tr_G3TBN4_G3TBN4_LOXAF_9785 are exactly identical! WARNING: Sequences sp_Q99M80_PTPRT_MOUSE_10090 and tr_A0A1U7UHI7_A0A1U7UHI7_TARSY_1868482 are exactly identical! WARNING: Sequences tr_M3Y0F5_M3Y0F5_MUSPF_9669 and tr_A0A2Y9ISK9_A0A2Y9ISK9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Y1R9_M3Y1R9_MUSPF_9669 and tr_G3SFI2_G3SFI2_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3Y1R9_M3Y1R9_MUSPF_9669 and tr_H0WN81_H0WN81_OTOGA_30611 are exactly identical! WARNING: Sequences tr_M3Y1R9_M3Y1R9_MUSPF_9669 and tr_A0A2Y9LHN4_A0A2Y9LHN4_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YC92_M3YC92_MUSPF_9669 and tr_G3QQV3_G3QQV3_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3YC92_M3YC92_MUSPF_9669 and tr_K7ETV1_K7ETV1_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3YC92_M3YC92_MUSPF_9669 and tr_G1TXJ3_G1TXJ3_RABIT_9986 are exactly identical! WARNING: Sequences tr_M3YC92_M3YC92_MUSPF_9669 and tr_E2R5J7_E2R5J7_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YC92_M3YC92_MUSPF_9669 and tr_H2RBP7_H2RBP7_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3YC92_M3YC92_MUSPF_9669 and tr_I3NAE1_I3NAE1_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3YC92_M3YC92_MUSPF_9669 and sp_P18433_PTPRA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3YC92_M3YC92_MUSPF_9669 and tr_F6TLA3_F6TLA3_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3YC92_M3YC92_MUSPF_9669 and tr_G5B4S5_G5B4S5_HETGA_10181 are exactly identical! WARNING: Sequences tr_M3YC92_M3YC92_MUSPF_9669 and tr_U3EAH6_U3EAH6_CALJA_9483 are exactly identical! WARNING: Sequences tr_M3YC92_M3YC92_MUSPF_9669 and tr_A0A287B8Q0_A0A287B8Q0_PIG_9823 are exactly identical! WARNING: Sequences tr_M3YC92_M3YC92_MUSPF_9669 and tr_G7PGU1_G7PGU1_MACFA_9541 are exactly identical! WARNING: Sequences tr_M3YC92_M3YC92_MUSPF_9669 and tr_A0A2I2V0E5_A0A2I2V0E5_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YC92_M3YC92_MUSPF_9669 and tr_A0A2I3NAL0_A0A2I3NAL0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3YC92_M3YC92_MUSPF_9669 and tr_A0A0D9RLM0_A0A0D9RLM0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3YC92_M3YC92_MUSPF_9669 and tr_A0A3Q0DFK3_A0A3Q0DFK3_TARSY_1868482 are exactly identical! WARNING: Sequences tr_M3YC92_M3YC92_MUSPF_9669 and tr_A0A2K5KVH8_A0A2K5KVH8_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3YC92_M3YC92_MUSPF_9669 and tr_A0A2K6BKY6_A0A2K6BKY6_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3YC92_M3YC92_MUSPF_9669 and tr_A0A2K5YT53_A0A2K5YT53_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3YC92_M3YC92_MUSPF_9669 and tr_A0A2R8ZSE8_A0A2R8ZSE8_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3YC92_M3YC92_MUSPF_9669 and tr_A0A2Y9IQU0_A0A2Y9IQU0_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YC92_M3YC92_MUSPF_9669 and tr_A0A384D361_A0A384D361_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3YQF3_M3YQF3_MUSPF_9669 and tr_A0A2Y9IX65_A0A2Y9IX65_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YT47_M3YT47_MUSPF_9669 and tr_W5PVQ2_W5PVQ2_SHEEP_9940 are exactly identical! WARNING: Sequences tr_M3YT47_M3YT47_MUSPF_9669 and tr_G1M815_G1M815_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YT47_M3YT47_MUSPF_9669 and tr_L5JPM6_L5JPM6_PTEAL_9402 are exactly identical! WARNING: Sequences tr_M3YT47_M3YT47_MUSPF_9669 and tr_A0A384C4Z1_A0A384C4Z1_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3YTU5_M3YTU5_MUSPF_9669 and tr_G1SE72_G1SE72_RABIT_9986 are exactly identical! WARNING: Sequences tr_M3YTU5_M3YTU5_MUSPF_9669 and tr_G1MEN5_G1MEN5_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YTU5_M3YTU5_MUSPF_9669 and tr_A0A337RYS5_A0A337RYS5_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YTU5_M3YTU5_MUSPF_9669 and tr_A0A2Y9KJM3_A0A2Y9KJM3_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YTU5_M3YTU5_MUSPF_9669 and tr_A0A384BZR4_A0A384BZR4_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2I3GK79_A0A2I3GK79_NOMLE_61853 and tr_H2NBZ5_H2NBZ5_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3GK79_A0A2I3GK79_NOMLE_61853 and tr_H2R3E7_H2R3E7_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3GK79_A0A2I3GK79_NOMLE_61853 and tr_A0A2R8ZB11_A0A2R8ZB11_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3HKZ8_A0A2I3HKZ8_NOMLE_61853 and sp_Q15262_PTPRK_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3HKZ8_A0A2I3HKZ8_NOMLE_61853 and tr_F7H7D9_F7H7D9_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3HKZ8_A0A2I3HKZ8_NOMLE_61853 and tr_A0A1U7T3U0_A0A1U7T3U0_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G1R5I4_G1R5I4_NOMLE_61853 and tr_A0A2I2ZFU2_A0A2I2ZFU2_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1R5I4_G1R5I4_NOMLE_61853 and tr_H2NVW2_H2NVW2_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1R5I4_G1R5I4_NOMLE_61853 and tr_H2QE85_H2QE85_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1R5I4_G1R5I4_NOMLE_61853 and tr_A0A287CYL6_A0A287CYL6_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G1R5I4_G1R5I4_NOMLE_61853 and sp_P28827_PTPRM_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1R5I4_G1R5I4_NOMLE_61853 and tr_A0A1D5Q4R1_A0A1D5Q4R1_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1R5I4_G1R5I4_NOMLE_61853 and tr_U3CYR3_U3CYR3_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1R5I4_G1R5I4_NOMLE_61853 and tr_G1LLN7_G1LLN7_AILME_9646 are exactly identical! WARNING: Sequences tr_G1R5I4_G1R5I4_NOMLE_61853 and tr_G7PWE3_G7PWE3_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1R5I4_G1R5I4_NOMLE_61853 and tr_L5K314_L5K314_PTEAL_9402 are exactly identical! WARNING: Sequences tr_G1R5I4_G1R5I4_NOMLE_61853 and tr_A0A2I2UR47_A0A2I2UR47_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1R5I4_G1R5I4_NOMLE_61853 and tr_A0A096N2E3_A0A096N2E3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1R5I4_G1R5I4_NOMLE_61853 and tr_A0A0D9RYA9_A0A0D9RYA9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1R5I4_G1R5I4_NOMLE_61853 and tr_A0A3Q0DSX5_A0A3Q0DSX5_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G1R5I4_G1R5I4_NOMLE_61853 and tr_A0A2K5LED7_A0A2K5LED7_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1R5I4_G1R5I4_NOMLE_61853 and tr_A0A2K6C632_A0A2K6C632_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1R5I4_G1R5I4_NOMLE_61853 and tr_A0A2K5ZT98_A0A2K5ZT98_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1R5I4_G1R5I4_NOMLE_61853 and tr_A0A2R8ZLI9_A0A2R8ZLI9_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1R5I4_G1R5I4_NOMLE_61853 and tr_A0A384C7G9_A0A384C7G9_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1S7F4_G1S7F4_NOMLE_61853 and tr_G3RJH5_G3RJH5_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S7F4_G1S7F4_NOMLE_61853 and tr_H2PS61_H2PS61_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1S7F4_G1S7F4_NOMLE_61853 and tr_F7D0E0_F7D0E0_HORSE_9796 are exactly identical! WARNING: Sequences tr_G1S7F4_G1S7F4_NOMLE_61853 and tr_W5PWC2_W5PWC2_SHEEP_9940 are exactly identical! WARNING: Sequences tr_G1S7F4_G1S7F4_NOMLE_61853 and tr_A0A287D609_A0A287D609_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G1S7F4_G1S7F4_NOMLE_61853 and tr_H0WXD2_H0WXD2_OTOGA_30611 are exactly identical! WARNING: Sequences tr_G1S7F4_G1S7F4_NOMLE_61853 and tr_H0V1B3_H0V1B3_CAVPO_10141 are exactly identical! WARNING: Sequences tr_G1S7F4_G1S7F4_NOMLE_61853 and tr_F7DWH2_F7DWH2_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1S7F4_G1S7F4_NOMLE_61853 and tr_G5BQG3_G5BQG3_HETGA_10181 are exactly identical! WARNING: Sequences tr_G1S7F4_G1S7F4_NOMLE_61853 and tr_F6RUY3_F6RUY3_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1S7F4_G1S7F4_NOMLE_61853 and tr_F1SMP2_F1SMP2_PIG_9823 are exactly identical! WARNING: Sequences tr_G1S7F4_G1S7F4_NOMLE_61853 and tr_G7PSD1_G7PSD1_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1S7F4_G1S7F4_NOMLE_61853 and tr_F1MJR2_F1MJR2_BOVIN_9913 are exactly identical! WARNING: Sequences tr_G1S7F4_G1S7F4_NOMLE_61853 and tr_L5K5N7_L5K5N7_PTEAL_9402 are exactly identical! WARNING: Sequences tr_G1S7F4_G1S7F4_NOMLE_61853 and tr_A0A2I3N9W3_A0A2I3N9W3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1S7F4_G1S7F4_NOMLE_61853 and tr_A0A0D9R9K5_A0A0D9R9K5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1S7F4_G1S7F4_NOMLE_61853 and tr_A0A2K5KQ07_A0A2K5KQ07_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1S7F4_G1S7F4_NOMLE_61853 and tr_A0A2K6A4P9_A0A2K6A4P9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1S7F4_G1S7F4_NOMLE_61853 and tr_A0A2R9AVC6_A0A2R9AVC6_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1S7F4_G1S7F4_NOMLE_61853 and tr_A0A2U3WBY4_A0A2U3WBY4_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1S7F4_G1S7F4_NOMLE_61853 and tr_A0A2U3XGP5_A0A2U3XGP5_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1S7F4_G1S7F4_NOMLE_61853 and tr_A0A2Y9FVZ6_A0A2Y9FVZ6_TRIMA_127582 are exactly identical! WARNING: Sequences tr_G1Q270_G1Q270_MYOLU_59463 and tr_L5K0K4_L5K0K4_PTEAL_9402 are exactly identical! WARNING: Sequences tr_G3HFG6_G3HFG6_CRIGR_10029 and tr_A0A1U8CHC3_A0A1U8CHC3_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A2I2YGJ3_A0A2I2YGJ3_GORGO_9595 and tr_H2P1Y8_H2P1Y8_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2YGJ3_A0A2I2YGJ3_GORGO_9595 and tr_H2R1K1_H2R1K1_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YGJ3_A0A2I2YGJ3_GORGO_9595 and sp_O14522_PTPRT_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2YGJ3_A0A2I2YGJ3_GORGO_9595 and tr_F6PVC0_F6PVC0_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I2YGJ3_A0A2I2YGJ3_GORGO_9595 and tr_A0A2I3MC75_A0A2I3MC75_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I2YGJ3_A0A2I2YGJ3_GORGO_9595 and tr_A0A0D9RNG5_A0A0D9RNG5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I2YGJ3_A0A2I2YGJ3_GORGO_9595 and tr_A0A2K6E5H2_A0A2K6E5H2_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I2YGJ3_A0A2I2YGJ3_GORGO_9595 and tr_A0A2K5YH94_A0A2K5YH94_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I2YGJ3_A0A2I2YGJ3_GORGO_9595 and tr_A0A2R9B7Y1_A0A2R9B7Y1_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2YYP7_A0A2I2YYP7_GORGO_9595 and tr_A0A2I3S9G7_A0A2I3S9G7_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YYP7_A0A2I2YYP7_GORGO_9595 and tr_F7H285_F7H285_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I2YYP7_A0A2I2YYP7_GORGO_9595 and tr_A0A2K6CKS1_A0A2K6CKS1_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I2YYP7_A0A2I2YYP7_GORGO_9595 and tr_A0A2R9BYW7_A0A2R9BYW7_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2N7P3_H2N7P3_PONAB_9601 and tr_G7NUX4_G7NUX4_MACFA_9541 are exactly identical! WARNING: Sequences tr_H2N7P3_H2N7P3_PONAB_9601 and tr_A0A0D9S7I9_A0A0D9S7I9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2N7P3_H2N7P3_PONAB_9601 and tr_A0A3Q0DQ14_A0A3Q0DQ14_TARSY_1868482 are exactly identical! WARNING: Sequences tr_H2N7P3_H2N7P3_PONAB_9601 and tr_A0A2K5NR41_A0A2K5NR41_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1NBY3_G1NBY3_MELGA_9103 and tr_A0A087RHH8_A0A087RHH8_APTFO_9233 are exactly identical! WARNING: Sequences tr_G1NBY3_G1NBY3_MELGA_9103 and tr_A0A093HZP7_A0A093HZP7_STRCA_441894 are exactly identical! WARNING: Sequences tr_G1NBY3_G1NBY3_MELGA_9103 and tr_A0A091VJT0_A0A091VJT0_OPIHO_30419 are exactly identical! WARNING: Sequences tr_G1NBY3_G1NBY3_MELGA_9103 and tr_A0A099ZNS1_A0A099ZNS1_TINGU_94827 are exactly identical! WARNING: Sequences tr_G1NBY3_G1NBY3_MELGA_9103 and tr_A0A0A0AGJ7_A0A0A0AGJ7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_G1NBY3_G1NBY3_MELGA_9103 and tr_A0A093IP48_A0A093IP48_DRYPU_118200 are exactly identical! WARNING: Sequences tr_G1NBY3_G1NBY3_MELGA_9103 and tr_A0A226NLC3_A0A226NLC3_CALSU_9009 are exactly identical! WARNING: Sequences tr_G1NBY3_G1NBY3_MELGA_9103 and tr_A0A226PJ14_A0A226PJ14_COLVI_9014 are exactly identical! WARNING: Sequences tr_G1NKM3_G1NKM3_MELGA_9103 and tr_A0A226NB73_A0A226NB73_CALSU_9009 are exactly identical! WARNING: Sequences tr_G1NKM3_G1NKM3_MELGA_9103 and tr_A0A226P275_A0A226P275_COLVI_9014 are exactly identical! WARNING: Sequences tr_G3UQ69_G3UQ69_MELGA_9103 and tr_U3ID46_U3ID46_ANAPL_8839 are exactly identical! WARNING: Sequences tr_G3UQ69_G3UQ69_MELGA_9103 and tr_A0A091JRG1_A0A091JRG1_EGRGA_188379 are exactly identical! WARNING: Sequences tr_G3UQ69_G3UQ69_MELGA_9103 and tr_A0A091VQ62_A0A091VQ62_NIPNI_128390 are exactly identical! WARNING: Sequences tr_G3UQ69_G3UQ69_MELGA_9103 and tr_A0A087RBA8_A0A087RBA8_APTFO_9233 are exactly identical! WARNING: Sequences tr_G3UQ69_G3UQ69_MELGA_9103 and tr_A0A093GT42_A0A093GT42_STRCA_441894 are exactly identical! WARNING: Sequences tr_G3UQ69_G3UQ69_MELGA_9103 and tr_A0A091GTY9_A0A091GTY9_9AVES_55661 are exactly identical! WARNING: Sequences tr_G3UQ69_G3UQ69_MELGA_9103 and tr_A0A2I0LQJ0_A0A2I0LQJ0_COLLI_8932 are exactly identical! WARNING: Sequences tr_G3UQ69_G3UQ69_MELGA_9103 and tr_A0A1V4KWQ8_A0A1V4KWQ8_PATFA_372326 are exactly identical! WARNING: Sequences tr_G1SFY2_G1SFY2_RABIT_9986 and tr_A0A2K6DKE5_A0A2K6DKE5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0R3NVE1_A0A0R3NVE1_DROPS_46245 and tr_B4GJB3_B4GJB3_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A2I3T7G8_A0A2I3T7G8_PANTR_9598 and tr_A0A2R9AE13_A0A2R9AE13_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QF28_H2QF28_PANTR_9598 and tr_F7HG97_F7HG97_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2QF28_H2QF28_PANTR_9598 and tr_F7IH26_F7IH26_CALJA_9483 are exactly identical! WARNING: Sequences tr_H2QF28_H2QF28_PANTR_9598 and tr_A0A2I3LET0_A0A2I3LET0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2QF28_H2QF28_PANTR_9598 and tr_A0A0D9RC69_A0A0D9RC69_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2QF28_H2QF28_PANTR_9598 and tr_A0A2K5NUE4_A0A2K5NUE4_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2QF28_H2QF28_PANTR_9598 and tr_A0A2K6CGE9_A0A2K6CGE9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A5I9F0_A5I9F0_RAT_10116 and tr_A0A1S3G0L0_A0A1S3G0L0_DIPOR_10020 are exactly identical! WARNING: Sequences tr_A0A3B5PUC8_A0A3B5PUC8_XIPMA_8083 and tr_A0A096M5L6_A0A096M5L6_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A088A887_A0A088A887_APIME_7460 and tr_A0A2A3E8K9_A0A2A3E8K9_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NJY1_A0A158NJY1_ATTCE_12957 and tr_F4WXQ1_F4WXQ1_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NJY1_A0A158NJY1_ATTCE_12957 and tr_A0A195BU66_A0A195BU66_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NJY1_A0A158NJY1_ATTCE_12957 and tr_A0A195F635_A0A195F635_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A158NJY1_A0A158NJY1_ATTCE_12957 and tr_A0A151IC73_A0A151IC73_9HYME_456900 are exactly identical! WARNING: Sequences tr_A0A286XJ97_A0A286XJ97_CAVPO_10141 and tr_A0A1S3ARM3_A0A1S3ARM3_ERIEU_9365 are exactly identical! WARNING: Sequences sp_P08575_PTPRC_HUMAN_9606 and tr_A0A2R9B4U9_A0A2R9B4U9_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7HTR9_F7HTR9_MACMU_9544 and tr_A0A2K5L5Q8_A0A2K5L5Q8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HTR9_F7HTR9_MACMU_9544 and tr_A0A2K6BMZ3_A0A2K6BMZ3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HTR9_F7HTR9_MACMU_9544 and tr_A0A2K5YHK1_A0A2K5YHK1_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0YR81_H0YR81_TAEGU_59729 and tr_A0A218UCG2_A0A218UCG2_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0Z360_H0Z360_TAEGU_59729 and tr_A0A218V9Q8_A0A218V9Q8_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZI52_H0ZI52_TAEGU_59729 and tr_A0A218UUU6_A0A218UUU6_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZND4_H0ZND4_TAEGU_59729 and tr_U3KAI1_U3KAI1_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0ZND4_H0ZND4_TAEGU_59729 and tr_A0A091VX05_A0A091VX05_OPIHO_30419 are exactly identical! WARNING: Sequences tr_H0ZND4_H0ZND4_TAEGU_59729 and tr_A0A091G8Y5_A0A091G8Y5_9AVES_55661 are exactly identical! WARNING: Sequences tr_H0ZND4_H0ZND4_TAEGU_59729 and tr_A0A2I0MVL2_A0A2I0MVL2_COLLI_8932 are exactly identical! WARNING: Sequences tr_H0ZND4_H0ZND4_TAEGU_59729 and tr_A0A1V4JLM7_A0A1V4JLM7_PATFA_372326 are exactly identical! WARNING: Sequences tr_G1LSC6_G1LSC6_AILME_9646 and tr_A0A2U3XIJ3_A0A2U3XIJ3_LEPWE_9713 are exactly identical! WARNING: Sequences tr_G1LSC6_G1LSC6_AILME_9646 and tr_A0A2Y9IUT8_A0A2Y9IUT8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1LSC6_G1LSC6_AILME_9646 and tr_A0A384CNU0_A0A384CNU0_URSMA_29073 are exactly identical! WARNING: Sequences tr_G7PEC8_G7PEC8_MACFA_9541 and tr_A0A2K6BYF7_A0A2K6BYF7_MACNE_9545 are exactly identical! WARNING: Sequences tr_L5KQB0_L5KQB0_PTEAL_9402 and tr_A0A383YP70_A0A383YP70_BALAS_310752 are exactly identical! WARNING: Sequences tr_U3JT91_U3JT91_FICAL_59894 and tr_A0A091HQ13_A0A091HQ13_CALAN_9244 are exactly identical! WARNING: Sequences tr_U3JT91_U3JT91_FICAL_59894 and tr_A0A1V4KMY5_A0A1V4KMY5_PATFA_372326 are exactly identical! WARNING: Sequences tr_U3I6U5_U3I6U5_ANAPL_8839 and tr_A0A151MY91_A0A151MY91_ALLMI_8496 are exactly identical! WARNING: Sequences tr_U3I6U5_U3I6U5_ANAPL_8839 and tr_A0A3Q0GDE4_A0A3Q0GDE4_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A087XZ60_A0A087XZ60_POEFO_48698 and tr_A0A096MBI7_A0A096MBI7_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A096N7E0_A0A096N7E0_PAPAN_9555 and tr_A0A2K5Y7Q0_A0A2K5Y7Q0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0D9QWP4_A0A0D9QWP4_CHLSB_60711 and tr_A0A2K5LWU5_A0A2K5LWU5_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A151M8L3_A0A151M8L3_ALLMI_8496 and tr_A0A3Q0G0Z8_A0A3Q0G0Z8_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NF49_A0A151NF49_ALLMI_8496 and tr_A0A1U8DE35_A0A1U8DE35_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151P044_A0A151P044_ALLMI_8496 and tr_A0A1U7SCF3_A0A1U7SCF3_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A0Q3PSP6_A0A0Q3PSP6_AMAAE_12930 and tr_A0A091IL26_A0A091IL26_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A0Q3PSP6_A0A0Q3PSP6_AMAAE_12930 and tr_A0A087QSE8_A0A087QSE8_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A0Q3PSP6_A0A0Q3PSP6_AMAAE_12930 and tr_A0A093GYZ2_A0A093GYZ2_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A0Q3PSP6_A0A0Q3PSP6_AMAAE_12930 and tr_A0A091XF21_A0A091XF21_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A0Q3PSP6_A0A0Q3PSP6_AMAAE_12930 and tr_A0A0A0AJF3_A0A0A0AJF3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0Q3PSP6_A0A0Q3PSP6_AMAAE_12930 and tr_A0A2I0MFV2_A0A2I0MFV2_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A091ERN5_A0A091ERN5_CORBR_85066 and tr_A0A091KAC9_A0A091KAC9_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A091ERN5_A0A091ERN5_CORBR_85066 and tr_A0A093PTS1_A0A093PTS1_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091ERN5_A0A091ERN5_CORBR_85066 and tr_A0A087RCB9_A0A087RCB9_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091EUP4_A0A091EUP4_CORBR_85066 and tr_A0A093Q0Y8_A0A093Q0Y8_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091FRH6_A0A091FRH6_CORBR_85066 and tr_A0A093PRQ0_A0A093PRQ0_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091ILL1_A0A091ILL1_EGRGA_188379 and tr_A0A091VJ01_A0A091VJ01_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091ILL1_A0A091ILL1_EGRGA_188379 and tr_A0A2I0MXP6_A0A2I0MXP6_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A091ILL1_A0A091ILL1_EGRGA_188379 and tr_A0A093G6U0_A0A093G6U0_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091JYG4_A0A091JYG4_EGRGA_188379 and tr_A0A091VPW3_A0A091VPW3_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JYG4_A0A091JYG4_EGRGA_188379 and tr_A0A087QN43_A0A087QN43_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JYG4_A0A091JYG4_EGRGA_188379 and tr_A0A091WFQ7_A0A091WFQ7_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091JYG4_A0A091JYG4_EGRGA_188379 and tr_A0A091GGS9_A0A091GGS9_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091JYG4_A0A091JYG4_EGRGA_188379 and tr_A0A0A0A9I1_A0A0A0A9I1_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091JYG4_A0A091JYG4_EGRGA_188379 and tr_A0A2I0MMG2_A0A2I0MMG2_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A091JYG4_A0A091JYG4_EGRGA_188379 and tr_A0A1V4JGL2_A0A1V4JGL2_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A091VVI6_A0A091VVI6_NIPNI_128390 and tr_A0A091I7Y5_A0A091I7Y5_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0V1D0A3_A0A0V1D0A3_TRIBR_45882 and tr_A0A0V0X4P3_A0A0V0X4P3_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1D0A3_A0A0V1D0A3_TRIBR_45882 and tr_A0A0V1LJV8_A0A0V1LJV8_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0VKN0_A0A0V0VKN0_9BILA_181606 and tr_A0A0V1P0D1_A0A0V1P0D1_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0VKN0_A0A0V0VKN0_9BILA_181606 and tr_A0A0V0UGC2_A0A0V0UGC2_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S3WRK2_A0A1S3WRK2_ERIEU_9365 and tr_A0A2Y9NAD7_A0A2Y9NAD7_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A1S3HQ46_A0A1S3HQ46_LINUN_7574 and tr_A0A1S3HQ57_A0A1S3HQ57_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3HQ46_A0A1S3HQ46_LINUN_7574 and tr_A0A1S3HQ62_A0A1S3HQ62_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3HQ46_A0A1S3HQ46_LINUN_7574 and tr_A0A1S3HRJ8_A0A1S3HRJ8_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3HQ46_A0A1S3HQ46_LINUN_7574 and tr_A0A1S3HSZ8_A0A1S3HSZ8_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3L819_A0A1S3L819_SALSA_8030 and tr_A0A060WA45_A0A060WA45_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A2D0QEJ7_A0A2D0QEJ7_ICTPU_7998 and tr_A0A2D0QFL7_A0A2D0QFL7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QEJ7_A0A2D0QEJ7_ICTPU_7998 and tr_A0A2D0QFM4_A0A2D0QFM4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QEJ7_A0A2D0QEJ7_ICTPU_7998 and tr_A0A2D0QH24_A0A2D0QH24_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RUP4_A0A2D0RUP4_ICTPU_7998 and tr_W5UBA6_W5UBA6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RWZ1_A0A2D0RWZ1_ICTPU_7998 and tr_A0A2D0RWZ5_A0A2D0RWZ5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RWZ1_A0A2D0RWZ1_ICTPU_7998 and tr_A0A2D0RXW6_A0A2D0RXW6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T9D0_A0A2D0T9D0_ICTPU_7998 and tr_A0A2D0T9D3_A0A2D0T9D3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T9D0_A0A2D0T9D0_ICTPU_7998 and tr_A0A2D0TA03_A0A2D0TA03_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4CLD7_A0A2U4CLD7_TURTR_9739 and tr_A0A2Y9PNW4_A0A2Y9PNW4_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CLD7_A0A2U4CLD7_TURTR_9739 and tr_A0A384B8A1_A0A384B8A1_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U4CNM5_A0A2U4CNM5_TURTR_9739 and tr_A0A2Y9SHY2_A0A2Y9SHY2_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4CNM5_A0A2U4CNM5_TURTR_9739 and tr_A0A384AUA1_A0A384AUA1_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9M0B4_A0A2Y9M0B4_DELLE_9749 and tr_A0A2Y9THR9_A0A2Y9THR9_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9M0B4_A0A2Y9M0B4_DELLE_9749 and tr_A0A383Z230_A0A383Z230_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9NJD0_A0A2Y9NJD0_DELLE_9749 and tr_A0A2Y9SVD7_A0A2Y9SVD7_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9NJD0_A0A2Y9NJD0_DELLE_9749 and tr_A0A383ZNV0_A0A383ZNV0_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9PY72_A0A2Y9PY72_DELLE_9749 and tr_A0A2Y9T5W4_A0A2Y9T5W4_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 220 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08575/3_mltree/P08575.raxml.reduced.phy Alignment comprises 1 partitions and 541 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 541 / 541 Gaps: 1.12 % Invariant sites: 0.37 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08575/3_mltree/P08575.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 7 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 78 / 6240 [00:00:00] Data distribution: max. searches per worker: 20 Starting ML tree search with 20 distinct starting trees [00:00:00 -812502.201172] Initial branch length optimization [00:00:03 -633892.598971] Model parameter optimization (eps = 10.000000) [00:00:28 -633355.296838] AUTODETECT spr round 1 (radius: 5) [00:01:57 -359385.730403] AUTODETECT spr round 2 (radius: 10) [00:03:30 -243811.033732] AUTODETECT spr round 3 (radius: 15) [00:05:10 -188510.208817] AUTODETECT spr round 4 (radius: 20) [00:06:54 -167002.275500] AUTODETECT spr round 5 (radius: 25) [00:08:48 -150792.508975] SPR radius for FAST iterations: 25 (autodetect) [00:08:48 -150792.508975] Model parameter optimization (eps = 3.000000) [00:09:04 -150588.173702] FAST spr round 1 (radius: 25) [00:10:40 -123733.936826] FAST spr round 2 (radius: 25) [00:11:57 -121165.958495] FAST spr round 3 (radius: 25) [00:13:09 -121004.956962] FAST spr round 4 (radius: 25) [00:14:17 -121003.765483] FAST spr round 5 (radius: 25) [00:15:22 -121003.764949] Model parameter optimization (eps = 1.000000) [00:15:34 -120998.975257] SLOW spr round 1 (radius: 5) [00:16:53 -120982.296458] SLOW spr round 2 (radius: 5) [00:18:10 -120980.795935] SLOW spr round 3 (radius: 5) [00:19:25 -120980.795804] SLOW spr round 4 (radius: 10) [00:20:46 -120979.255506] SLOW spr round 5 (radius: 5) [00:22:17 -120979.255375] SLOW spr round 6 (radius: 10) [00:23:44 -120979.255374] SLOW spr round 7 (radius: 15) [00:25:29 -120979.255374] SLOW spr round 8 (radius: 20) [00:28:11 -120979.255374] SLOW spr round 9 (radius: 25) [00:31:26 -120979.255374] Model parameter optimization (eps = 0.100000) [00:31:31] ML tree search #1, logLikelihood: -120979.215540 [00:31:31 -807490.176822] Initial branch length optimization [00:31:33 -630893.916519] Model parameter optimization (eps = 10.000000) [00:31:56 -630269.621091] AUTODETECT spr round 1 (radius: 5) [00:33:24 -359199.058480] AUTODETECT spr round 2 (radius: 10) [00:34:58 -235263.877656] AUTODETECT spr round 3 (radius: 15) [00:36:35 -166650.793802] AUTODETECT spr round 4 (radius: 20) [00:38:14 -146721.541904] AUTODETECT spr round 5 (radius: 25) [00:40:07 -141581.028864] SPR radius for FAST iterations: 25 (autodetect) [00:40:07 -141581.028864] Model parameter optimization (eps = 3.000000) [00:40:22 -141439.523303] FAST spr round 1 (radius: 25) [00:41:54 -122310.681592] FAST spr round 2 (radius: 25) [00:43:11 -121128.768218] FAST spr round 3 (radius: 25) [00:44:21 -121053.851093] FAST spr round 4 (radius: 25) [00:45:27 -121053.851061] Model parameter optimization (eps = 1.000000) [00:45:38 -121023.547951] SLOW spr round 1 (radius: 5) [00:46:59 -120955.719909] SLOW spr round 2 (radius: 5) [00:48:20 -120944.814599] SLOW spr round 3 (radius: 5) [00:49:40 -120942.423281] SLOW spr round 4 (radius: 5) [00:50:59 -120942.422852] SLOW spr round 5 (radius: 10) [00:52:23 -120940.004834] SLOW spr round 6 (radius: 5) [00:53:56 -120940.004753] SLOW spr round 7 (radius: 10) [00:55:25 -120940.004700] SLOW spr round 8 (radius: 15) [00:57:12 -120940.004699] SLOW spr round 9 (radius: 20) [01:00:01 -120940.004698] SLOW spr round 10 (radius: 25) [01:03:29 -120940.004697] Model parameter optimization (eps = 0.100000) [01:03:36] ML tree search #2, logLikelihood: -120939.844373 [01:03:36 -814692.103686] Initial branch length optimization [01:03:38 -638744.938347] Model parameter optimization (eps = 10.000000) [01:03:53 -638210.864516] AUTODETECT spr round 1 (radius: 5) [01:05:26 -343280.353536] AUTODETECT spr round 2 (radius: 10) [01:07:05 -231971.269397] AUTODETECT spr round 3 (radius: 15) [01:08:49 -176120.227677] AUTODETECT spr round 4 (radius: 20) [01:10:43 -151887.602765] AUTODETECT spr round 5 (radius: 25) [01:12:47 -143655.425289] SPR radius for FAST iterations: 25 (autodetect) [01:12:47 -143655.425289] Model parameter optimization (eps = 3.000000) [01:13:07 -143432.769258] FAST spr round 1 (radius: 25) [01:14:43 -122227.913632] FAST spr round 2 (radius: 25) [01:16:00 -121147.021651] FAST spr round 3 (radius: 25) [01:17:13 -121028.040526] FAST spr round 4 (radius: 25) [01:18:23 -121015.947532] FAST spr round 5 (radius: 25) [01:19:30 -121015.475821] FAST spr round 6 (radius: 25) [01:20:35 -121015.475813] Model parameter optimization (eps = 1.000000) [01:20:45 -120999.876470] SLOW spr round 1 (radius: 5) [01:22:05 -120973.197586] SLOW spr round 2 (radius: 5) [01:23:23 -120973.191689] SLOW spr round 3 (radius: 10) [01:24:43 -120973.191669] SLOW spr round 4 (radius: 15) [01:26:33 -120973.191636] SLOW spr round 5 (radius: 20) [01:29:10 -120973.191636] SLOW spr round 6 (radius: 25) [01:32:33 -120973.191636] Model parameter optimization (eps = 0.100000) [01:32:39] ML tree search #3, logLikelihood: -120973.076510 [01:32:39 -811073.770886] Initial branch length optimization [01:32:42 -636563.258050] Model parameter optimization (eps = 10.000000) [01:33:06 -635885.702333] AUTODETECT spr round 1 (radius: 5) [01:34:37 -360703.436577] AUTODETECT spr round 2 (radius: 10) [01:36:15 -220127.307512] AUTODETECT spr round 3 (radius: 15) [01:37:49 -168470.228778] AUTODETECT spr round 4 (radius: 20) [01:39:34 -149753.606881] AUTODETECT spr round 5 (radius: 25) [01:41:29 -142157.114979] SPR radius for FAST iterations: 25 (autodetect) [01:41:29 -142157.114979] Model parameter optimization (eps = 3.000000) [01:41:46 -141969.358295] FAST spr round 1 (radius: 25) [01:43:21 -123109.198116] FAST spr round 2 (radius: 25) [01:44:38 -121104.703397] FAST spr round 3 (radius: 25) [01:45:49 -121045.952279] FAST spr round 4 (radius: 25) [01:46:57 -121043.208168] FAST spr round 5 (radius: 25) [01:48:04 -121043.208072] Model parameter optimization (eps = 1.000000) [01:48:13 -121026.216639] SLOW spr round 1 (radius: 5) [01:49:33 -120985.429115] SLOW spr round 2 (radius: 5) [01:50:54 -120980.947615] SLOW spr round 3 (radius: 5) [01:52:14 -120979.116643] SLOW spr round 4 (radius: 5) [01:53:33 -120979.116419] SLOW spr round 5 (radius: 10) [01:54:56 -120979.116386] SLOW spr round 6 (radius: 15) [01:56:49 -120979.116369] SLOW spr round 7 (radius: 20) [01:59:31 -120979.116367] SLOW spr round 8 (radius: 25) [02:02:54 -120979.116367] Model parameter optimization (eps = 0.100000) [02:03:02] ML tree search #4, logLikelihood: -120978.543438 [02:03:02 -817437.902592] Initial branch length optimization [02:03:04 -639016.041752] Model parameter optimization (eps = 10.000000) [02:03:27 -638383.026936] AUTODETECT spr round 1 (radius: 5) [02:04:59 -370476.898987] AUTODETECT spr round 2 (radius: 10) [02:06:38 -235407.171836] AUTODETECT spr round 3 (radius: 15) [02:08:17 -168623.363617] AUTODETECT spr round 4 (radius: 20) [02:10:00 -147855.128002] AUTODETECT spr round 5 (radius: 25) [02:12:02 -141760.159382] SPR radius for FAST iterations: 25 (autodetect) [02:12:02 -141760.159382] Model parameter optimization (eps = 3.000000) [02:12:23 -141541.886794] FAST spr round 1 (radius: 25) [02:14:01 -122020.621585] FAST spr round 2 (radius: 25) [02:15:22 -121105.255083] FAST spr round 3 (radius: 25) [02:16:35 -121049.669485] FAST spr round 4 (radius: 25) [02:17:45 -121032.639749] FAST spr round 5 (radius: 25) [02:18:52 -121016.790952] FAST spr round 6 (radius: 25) [02:19:58 -121014.874015] FAST spr round 7 (radius: 25) [02:21:03 -121014.874011] Model parameter optimization (eps = 1.000000) [02:21:12 -121012.430289] SLOW spr round 1 (radius: 5) [02:22:31 -120971.913742] SLOW spr round 2 (radius: 5) [02:23:49 -120964.465942] SLOW spr round 3 (radius: 5) [02:25:09 -120962.277256] SLOW spr round 4 (radius: 5) [02:26:27 -120962.277148] SLOW spr round 5 (radius: 10) [02:27:50 -120961.946256] SLOW spr round 6 (radius: 5) [02:29:26 -120958.949032] SLOW spr round 7 (radius: 5) [02:30:52 -120956.035954] SLOW spr round 8 (radius: 5) [02:32:12 -120956.035885] SLOW spr round 9 (radius: 10) [02:33:34 -120956.035883] SLOW spr round 10 (radius: 15) [02:35:23 -120956.035880] SLOW spr round 11 (radius: 20) [02:38:01 -120956.035879] SLOW spr round 12 (radius: 25) [02:41:28 -120956.035877] Model parameter optimization (eps = 0.100000) [02:41:36] ML tree search #5, logLikelihood: -120955.682398 [02:41:36 -812278.805343] Initial branch length optimization [02:41:39 -636878.357313] Model parameter optimization (eps = 10.000000) [02:41:55 -636280.389745] AUTODETECT spr round 1 (radius: 5) [02:43:27 -369320.646374] AUTODETECT spr round 2 (radius: 10) [02:45:02 -236118.825771] AUTODETECT spr round 3 (radius: 15) [02:46:42 -183921.163307] AUTODETECT spr round 4 (radius: 20) [02:48:24 -167847.065811] AUTODETECT spr round 5 (radius: 25) [02:50:22 -160954.909745] SPR radius for FAST iterations: 25 (autodetect) [02:50:22 -160954.909745] Model parameter optimization (eps = 3.000000) [02:50:40 -160697.324476] FAST spr round 1 (radius: 25) [02:52:17 -124778.268262] FAST spr round 2 (radius: 25) [02:53:36 -121265.241165] FAST spr round 3 (radius: 25) [02:54:49 -121047.358364] FAST spr round 4 (radius: 25) [02:55:57 -121043.358491] FAST spr round 5 (radius: 25) [02:57:03 -121041.474122] FAST spr round 6 (radius: 25) [02:58:08 -121041.474094] Model parameter optimization (eps = 1.000000) [02:58:18 -121023.998763] SLOW spr round 1 (radius: 5) [02:59:38 -120984.533539] SLOW spr round 2 (radius: 5) [03:00:58 -120977.502988] SLOW spr round 3 (radius: 5) [03:02:16 -120974.958390] SLOW spr round 4 (radius: 5) [03:03:34 -120974.958291] SLOW spr round 5 (radius: 10) [03:04:57 -120974.896957] SLOW spr round 6 (radius: 15) [03:06:46 -120974.896953] SLOW spr round 7 (radius: 20) [03:09:27 -120974.896952] SLOW spr round 8 (radius: 25) [03:12:43 -120974.896951] Model parameter optimization (eps = 0.100000) [03:12:50] ML tree search #6, logLikelihood: -120974.796093 [03:12:50 -809643.169799] Initial branch length optimization [03:12:53 -635973.837594] Model parameter optimization (eps = 10.000000) [03:13:21 -635309.727428] AUTODETECT spr round 1 (radius: 5) [03:14:52 -350105.790398] AUTODETECT spr round 2 (radius: 10) [03:16:28 -229095.785109] AUTODETECT spr round 3 (radius: 15) [03:18:03 -186950.430137] AUTODETECT spr round 4 (radius: 20) [03:19:52 -159469.505939] AUTODETECT spr round 5 (radius: 25) [03:21:42 -144837.488190] SPR radius for FAST iterations: 25 (autodetect) [03:21:42 -144837.488190] Model parameter optimization (eps = 3.000000) [03:22:04 -144650.181400] FAST spr round 1 (radius: 25) [03:23:39 -123126.742151] FAST spr round 2 (radius: 25) [03:24:56 -121157.025672] FAST spr round 3 (radius: 25) [03:26:09 -121058.097074] FAST spr round 4 (radius: 25) [03:27:20 -121039.842018] FAST spr round 5 (radius: 25) [03:28:28 -121036.052873] FAST spr round 6 (radius: 25) [03:29:33 -121034.553084] FAST spr round 7 (radius: 25) [03:30:38 -121034.553027] Model parameter optimization (eps = 1.000000) [03:30:49 -121019.204606] SLOW spr round 1 (radius: 5) [03:32:08 -120974.575133] SLOW spr round 2 (radius: 5) [03:33:28 -120971.506627] SLOW spr round 3 (radius: 5) [03:34:45 -120971.506335] SLOW spr round 4 (radius: 10) [03:36:07 -120971.506329] SLOW spr round 5 (radius: 15) [03:37:57 -120971.506329] SLOW spr round 6 (radius: 20) [03:40:38 -120971.506291] SLOW spr round 7 (radius: 25) [03:43:56 -120971.506291] Model parameter optimization (eps = 0.100000) [03:44:05] ML tree search #7, logLikelihood: -120969.176468 [03:44:05 -812493.651174] Initial branch length optimization [03:44:08 -630543.416482] Model parameter optimization (eps = 10.000000) [03:44:37 -629896.690096] AUTODETECT spr round 1 (radius: 5) [03:46:09 -360098.359659] AUTODETECT spr round 2 (radius: 10) [03:47:45 -234324.865850] AUTODETECT spr round 3 (radius: 15) [03:49:27 -182938.878977] AUTODETECT spr round 4 (radius: 20) [03:51:15 -144992.316090] AUTODETECT spr round 5 (radius: 25) [03:53:06 -140855.300636] SPR radius for FAST iterations: 25 (autodetect) [03:53:06 -140855.300636] Model parameter optimization (eps = 3.000000) [03:53:24 -140621.775080] FAST spr round 1 (radius: 25) [03:55:00 -122662.104898] FAST spr round 2 (radius: 25) [03:56:23 -121109.986727] FAST spr round 3 (radius: 25) [03:57:36 -121023.158956] FAST spr round 4 (radius: 25) [03:58:45 -121017.398668] FAST spr round 5 (radius: 25) [03:59:51 -121017.398364] Model parameter optimization (eps = 1.000000) [04:00:01 -120995.552668] SLOW spr round 1 (radius: 5) [04:01:22 -120970.468359] SLOW spr round 2 (radius: 5) [04:02:42 -120959.024520] SLOW spr round 3 (radius: 5) [04:04:01 -120956.560746] SLOW spr round 4 (radius: 5) [04:05:20 -120956.560630] SLOW spr round 5 (radius: 10) [04:06:42 -120955.718296] SLOW spr round 6 (radius: 5) [04:08:15 -120953.013494] SLOW spr round 7 (radius: 5) [04:09:40 -120952.760397] SLOW spr round 8 (radius: 5) [04:11:00 -120952.760388] SLOW spr round 9 (radius: 10) [04:12:22 -120952.760387] SLOW spr round 10 (radius: 15) [04:14:13 -120952.760387] SLOW spr round 11 (radius: 20) [04:16:51 -120952.760387] SLOW spr round 12 (radius: 25) [04:20:17 -120952.760387] Model parameter optimization (eps = 0.100000) [04:20:24] ML tree search #8, logLikelihood: -120952.652493 [04:20:24 -819084.199198] Initial branch length optimization [04:20:26 -642067.788640] Model parameter optimization (eps = 10.000000) [04:20:46 -641477.087949] AUTODETECT spr round 1 (radius: 5) [04:22:17 -350456.871200] AUTODETECT spr round 2 (radius: 10) [04:23:51 -236100.274413] AUTODETECT spr round 3 (radius: 15) [04:25:36 -175909.685654] AUTODETECT spr round 4 (radius: 20) [04:27:34 -146490.297869] AUTODETECT spr round 5 (radius: 25) [04:29:42 -140581.773352] SPR radius for FAST iterations: 25 (autodetect) [04:29:42 -140581.773352] Model parameter optimization (eps = 3.000000) [04:30:00 -140392.524582] FAST spr round 1 (radius: 25) [04:31:38 -122843.630490] FAST spr round 2 (radius: 25) [04:32:57 -121148.412373] FAST spr round 3 (radius: 25) [04:34:09 -121045.534867] FAST spr round 4 (radius: 25) [04:35:19 -121013.247227] FAST spr round 5 (radius: 25) [04:36:25 -121013.244927] Model parameter optimization (eps = 1.000000) [04:36:36 -120987.885591] SLOW spr round 1 (radius: 5) [04:37:57 -120952.150747] SLOW spr round 2 (radius: 5) [04:39:15 -120950.317155] SLOW spr round 3 (radius: 5) [04:40:32 -120950.316873] SLOW spr round 4 (radius: 10) [04:41:54 -120948.491795] SLOW spr round 5 (radius: 5) [04:43:26 -120948.491323] SLOW spr round 6 (radius: 10) [04:44:54 -120948.491261] SLOW spr round 7 (radius: 15) [04:46:39 -120948.491217] SLOW spr round 8 (radius: 20) [04:49:32 -120948.491216] SLOW spr round 9 (radius: 25) [04:53:00 -120948.491216] Model parameter optimization (eps = 0.100000) [04:53:06] ML tree search #9, logLikelihood: -120948.313458 [04:53:06 -809405.730637] Initial branch length optimization [04:53:09 -634893.105865] Model parameter optimization (eps = 10.000000) [04:53:28 -634260.082844] AUTODETECT spr round 1 (radius: 5) [04:54:59 -370019.180954] AUTODETECT spr round 2 (radius: 10) [04:56:36 -216533.772407] AUTODETECT spr round 3 (radius: 15) [04:58:09 -170823.530116] AUTODETECT spr round 4 (radius: 20) [04:59:56 -149169.936919] AUTODETECT spr round 5 (radius: 25) [05:02:04 -138835.423832] SPR radius for FAST iterations: 25 (autodetect) [05:02:04 -138835.423832] Model parameter optimization (eps = 3.000000) [05:02:22 -138648.537803] FAST spr round 1 (radius: 25) [05:04:02 -122452.277570] FAST spr round 2 (radius: 25) [05:05:23 -121244.330870] FAST spr round 3 (radius: 25) [05:06:35 -121046.632262] FAST spr round 4 (radius: 25) [05:07:45 -121035.555151] FAST spr round 5 (radius: 25) [05:08:52 -121033.099553] FAST spr round 6 (radius: 25) [05:09:56 -121033.099270] Model parameter optimization (eps = 1.000000) [05:10:07 -121001.908591] SLOW spr round 1 (radius: 5) [05:11:26 -120959.750196] SLOW spr round 2 (radius: 5) [05:12:45 -120953.675664] SLOW spr round 3 (radius: 5) [05:14:04 -120952.114783] SLOW spr round 4 (radius: 5) [05:15:23 -120952.114559] SLOW spr round 5 (radius: 10) [05:16:45 -120951.380706] SLOW spr round 6 (radius: 5) [05:18:17 -120951.380040] SLOW spr round 7 (radius: 10) [05:19:45 -120951.379999] SLOW spr round 8 (radius: 15) [05:21:30 -120951.379992] SLOW spr round 9 (radius: 20) [05:24:12 -120951.379992] SLOW spr round 10 (radius: 25) [05:27:37 -120951.379992] Model parameter optimization (eps = 0.100000) [05:27:45] ML tree search #10, logLikelihood: -120950.866100 [05:27:46 -815300.747756] Initial branch length optimization [05:27:48 -635676.221142] Model parameter optimization (eps = 10.000000) [05:28:08 -635109.202714] AUTODETECT spr round 1 (radius: 5) [05:29:38 -359428.670469] AUTODETECT spr round 2 (radius: 10) [05:31:14 -231281.939206] AUTODETECT spr round 3 (radius: 15) [05:32:54 -171112.315293] AUTODETECT spr round 4 (radius: 20) [05:34:39 -152116.612691] AUTODETECT spr round 5 (radius: 25) [05:36:38 -143841.643966] SPR radius for FAST iterations: 25 (autodetect) [05:36:38 -143841.643966] Model parameter optimization (eps = 3.000000) [05:36:58 -143674.888567] FAST spr round 1 (radius: 25) [05:38:39 -122754.668513] FAST spr round 2 (radius: 25) [05:40:03 -121141.246698] FAST spr round 3 (radius: 25) [05:41:19 -121075.928004] FAST spr round 4 (radius: 25) [05:42:29 -121057.765879] FAST spr round 5 (radius: 25) [05:43:35 -121057.048889] FAST spr round 6 (radius: 25) [05:44:40 -121054.051668] FAST spr round 7 (radius: 25) [05:45:45 -121054.051638] Model parameter optimization (eps = 1.000000) [05:45:56 -121020.166356] SLOW spr round 1 (radius: 5) [05:47:18 -120978.415793] SLOW spr round 2 (radius: 5) [05:48:37 -120970.560106] SLOW spr round 3 (radius: 5) [05:49:56 -120969.126788] SLOW spr round 4 (radius: 5) [05:51:12 -120969.126463] SLOW spr round 5 (radius: 10) [05:52:35 -120958.116420] SLOW spr round 6 (radius: 5) [05:54:08 -120958.116236] SLOW spr round 7 (radius: 10) [05:55:36 -120958.116234] SLOW spr round 8 (radius: 15) [05:57:24 -120958.116234] SLOW spr round 9 (radius: 20) [06:00:10 -120958.116234] SLOW spr round 10 (radius: 25) [06:03:30 -120958.116234] Model parameter optimization (eps = 0.100000) [06:03:38] ML tree search #11, logLikelihood: -120957.914225 [06:03:38 -815387.178334] Initial branch length optimization [06:03:40 -636468.123266] Model parameter optimization (eps = 10.000000) [06:04:00 -635905.739843] AUTODETECT spr round 1 (radius: 5) [06:05:29 -360466.429599] AUTODETECT spr round 2 (radius: 10) [06:07:05 -222534.981930] AUTODETECT spr round 3 (radius: 15) [06:08:38 -168453.647870] AUTODETECT spr round 4 (radius: 20) [06:10:17 -149804.371901] AUTODETECT spr round 5 (radius: 25) [06:12:14 -146408.016228] SPR radius for FAST iterations: 25 (autodetect) [06:12:14 -146408.016228] Model parameter optimization (eps = 3.000000) [06:12:30 -146210.534638] FAST spr round 1 (radius: 25) [06:14:09 -122382.333094] FAST spr round 2 (radius: 25) [06:15:32 -121109.076138] FAST spr round 3 (radius: 25) [06:16:45 -121049.535269] FAST spr round 4 (radius: 25) [06:17:53 -121046.633569] FAST spr round 5 (radius: 25) [06:18:59 -121046.633507] Model parameter optimization (eps = 1.000000) [06:19:11 -121009.487965] SLOW spr round 1 (radius: 5) [06:20:35 -120966.722779] SLOW spr round 2 (radius: 5) [06:21:55 -120963.939473] SLOW spr round 3 (radius: 5) [06:23:15 -120963.933289] SLOW spr round 4 (radius: 10) [06:24:37 -120963.932366] SLOW spr round 5 (radius: 15) [06:26:32 -120963.932116] SLOW spr round 6 (radius: 20) [06:29:16 -120963.932094] SLOW spr round 7 (radius: 25) [06:32:50 -120963.932091] Model parameter optimization (eps = 0.100000) [06:32:56] ML tree search #12, logLikelihood: -120963.841416 [06:32:56 -808012.300225] Initial branch length optimization [06:32:58 -632705.759690] Model parameter optimization (eps = 10.000000) [06:33:19 -632135.872021] AUTODETECT spr round 1 (radius: 5) [06:34:49 -367865.666100] AUTODETECT spr round 2 (radius: 10) [06:36:24 -235645.593687] AUTODETECT spr round 3 (radius: 15) [06:38:08 -173986.850053] AUTODETECT spr round 4 (radius: 20) [06:39:55 -150954.601885] AUTODETECT spr round 5 (radius: 25) [06:41:54 -144254.329892] SPR radius for FAST iterations: 25 (autodetect) [06:41:54 -144254.329892] Model parameter optimization (eps = 3.000000) [06:42:11 -144018.924495] FAST spr round 1 (radius: 25) [06:43:46 -123660.139813] FAST spr round 2 (radius: 25) [06:45:04 -121571.440567] FAST spr round 3 (radius: 25) [06:46:16 -121053.318596] FAST spr round 4 (radius: 25) [06:47:26 -121012.181200] FAST spr round 5 (radius: 25) [06:48:32 -121012.181117] Model parameter optimization (eps = 1.000000) [06:48:39 -121006.889768] SLOW spr round 1 (radius: 5) [06:49:59 -120956.373847] SLOW spr round 2 (radius: 5) [06:51:19 -120952.168631] SLOW spr round 3 (radius: 5) [06:52:37 -120952.116328] SLOW spr round 4 (radius: 10) [06:53:58 -120951.506789] SLOW spr round 5 (radius: 5) [06:55:31 -120951.238027] SLOW spr round 6 (radius: 5) [06:56:55 -120951.237800] SLOW spr round 7 (radius: 10) [06:58:19 -120951.237798] SLOW spr round 8 (radius: 15) [07:00:08 -120951.237798] SLOW spr round 9 (radius: 20) [07:02:54 -120951.237797] SLOW spr round 10 (radius: 25) [07:06:11 -120951.237797] Model parameter optimization (eps = 0.100000) [07:06:15] ML tree search #13, logLikelihood: -120951.163931 [07:06:15 -810943.055963] Initial branch length optimization [07:06:17 -637741.718677] Model parameter optimization (eps = 10.000000) [07:06:37 -637119.731930] AUTODETECT spr round 1 (radius: 5) [07:08:07 -352123.862344] AUTODETECT spr round 2 (radius: 10) [07:09:41 -223192.585156] AUTODETECT spr round 3 (radius: 15) [07:11:26 -156514.272128] AUTODETECT spr round 4 (radius: 20) [07:13:10 -145392.817668] AUTODETECT spr round 5 (radius: 25) [07:15:15 -141229.269252] SPR radius for FAST iterations: 25 (autodetect) [07:15:15 -141229.269252] Model parameter optimization (eps = 3.000000) [07:15:32 -141078.104971] FAST spr round 1 (radius: 25) [07:17:04 -122858.871870] FAST spr round 2 (radius: 25) [07:18:21 -121333.363530] FAST spr round 3 (radius: 25) [07:19:34 -121155.146418] FAST spr round 4 (radius: 25) [07:20:43 -121081.497875] FAST spr round 5 (radius: 25) [07:21:51 -121060.328546] FAST spr round 6 (radius: 25) [07:22:57 -121050.254296] FAST spr round 7 (radius: 25) [07:24:02 -121050.254193] Model parameter optimization (eps = 1.000000) [07:24:13 -121003.155179] SLOW spr round 1 (radius: 5) [07:25:32 -120968.832882] SLOW spr round 2 (radius: 5) [07:26:52 -120961.956426] SLOW spr round 3 (radius: 5) [07:28:11 -120953.440440] SLOW spr round 4 (radius: 5) [07:29:30 -120949.961119] SLOW spr round 5 (radius: 5) [07:30:49 -120949.960860] SLOW spr round 6 (radius: 10) [07:32:10 -120949.521871] SLOW spr round 7 (radius: 5) [07:33:42 -120949.516501] SLOW spr round 8 (radius: 10) [07:35:09 -120949.516466] SLOW spr round 9 (radius: 15) [07:36:56 -120949.516465] SLOW spr round 10 (radius: 20) [07:39:40 -120949.516464] SLOW spr round 11 (radius: 25) [07:43:07 -120949.516463] Model parameter optimization (eps = 0.100000) [07:43:15] ML tree search #14, logLikelihood: -120949.221360 [07:43:15 -805220.387171] Initial branch length optimization [07:43:18 -629203.030164] Model parameter optimization (eps = 10.000000) [07:43:37 -628633.377928] AUTODETECT spr round 1 (radius: 5) [07:45:08 -363792.439958] AUTODETECT spr round 2 (radius: 10) [07:46:43 -230018.659506] AUTODETECT spr round 3 (radius: 15) [07:48:20 -171881.319911] AUTODETECT spr round 4 (radius: 20) [07:50:11 -145819.368234] AUTODETECT spr round 5 (radius: 25) [07:52:08 -141610.219920] SPR radius for FAST iterations: 25 (autodetect) [07:52:08 -141610.219920] Model parameter optimization (eps = 3.000000) [07:52:28 -141386.953359] FAST spr round 1 (radius: 25) [07:54:07 -122434.870225] FAST spr round 2 (radius: 25) [07:55:26 -121144.818988] FAST spr round 3 (radius: 25) [07:56:40 -121085.923243] FAST spr round 4 (radius: 25) [07:57:50 -121055.946834] FAST spr round 5 (radius: 25) [07:58:56 -121055.946701] Model parameter optimization (eps = 1.000000) [07:59:07 -121040.979826] SLOW spr round 1 (radius: 5) [08:00:30 -120989.158045] SLOW spr round 2 (radius: 5) [08:01:51 -120969.083809] SLOW spr round 3 (radius: 5) [08:03:10 -120969.083053] SLOW spr round 4 (radius: 10) [08:04:34 -120967.185798] SLOW spr round 5 (radius: 5) [08:06:07 -120967.185314] SLOW spr round 6 (radius: 10) [08:07:34 -120967.185274] SLOW spr round 7 (radius: 15) [08:09:18 -120967.185269] SLOW spr round 8 (radius: 20) [08:11:59 -120967.185269] SLOW spr round 9 (radius: 25) [08:15:20 -120967.185269] Model parameter optimization (eps = 0.100000) [08:15:25] ML tree search #15, logLikelihood: -120967.092271 [08:15:25 -815266.243888] Initial branch length optimization [08:15:29 -638826.588708] Model parameter optimization (eps = 10.000000) [08:15:47 -638244.299805] AUTODETECT spr round 1 (radius: 5) [08:17:17 -353226.132328] AUTODETECT spr round 2 (radius: 10) [08:18:51 -236717.871932] AUTODETECT spr round 3 (radius: 15) [08:20:36 -172386.467066] AUTODETECT spr round 4 (radius: 20) [08:22:19 -150517.836538] AUTODETECT spr round 5 (radius: 25) [08:24:30 -139871.991567] SPR radius for FAST iterations: 25 (autodetect) [08:24:30 -139871.991567] Model parameter optimization (eps = 3.000000) [08:24:54 -139669.056008] FAST spr round 1 (radius: 25) [08:26:31 -122258.470364] FAST spr round 2 (radius: 25) [08:27:48 -121079.380485] FAST spr round 3 (radius: 25) [08:29:02 -120998.617961] FAST spr round 4 (radius: 25) [08:30:10 -120995.933235] FAST spr round 5 (radius: 25) [08:31:17 -120993.088815] FAST spr round 6 (radius: 25) [08:32:21 -120993.088689] Model parameter optimization (eps = 1.000000) [08:32:31 -120990.361797] SLOW spr round 1 (radius: 5) [08:33:49 -120956.895221] SLOW spr round 2 (radius: 5) [08:35:09 -120956.846468] SLOW spr round 3 (radius: 10) [08:36:32 -120956.564076] SLOW spr round 4 (radius: 5) [08:38:06 -120956.563300] SLOW spr round 5 (radius: 10) [08:39:33 -120956.563292] SLOW spr round 6 (radius: 15) [08:41:19 -120956.563292] SLOW spr round 7 (radius: 20) [08:44:02 -120956.563292] SLOW spr round 8 (radius: 25) [08:47:29 -120956.563292] Model parameter optimization (eps = 0.100000) [08:47:32] ML tree search #16, logLikelihood: -120956.533831 [08:47:32 -816057.561800] Initial branch length optimization [08:47:35 -639129.117173] Model parameter optimization (eps = 10.000000) [08:48:00 -638573.816779] AUTODETECT spr round 1 (radius: 5) [08:49:30 -354899.507514] AUTODETECT spr round 2 (radius: 10) [08:51:07 -229318.443146] AUTODETECT spr round 3 (radius: 15) [08:52:38 -174191.347659] AUTODETECT spr round 4 (radius: 20) [08:54:29 -151271.730230] AUTODETECT spr round 5 (radius: 25) [08:56:22 -146518.327263] SPR radius for FAST iterations: 25 (autodetect) [08:56:22 -146518.327263] Model parameter optimization (eps = 3.000000) [08:56:41 -146329.271596] FAST spr round 1 (radius: 25) [08:58:11 -122068.304090] FAST spr round 2 (radius: 25) [08:59:27 -121163.663706] FAST spr round 3 (radius: 25) [09:00:39 -121058.356154] FAST spr round 4 (radius: 25) [09:01:46 -121056.363821] FAST spr round 5 (radius: 25) [09:02:52 -121054.483885] FAST spr round 6 (radius: 25) [09:03:57 -121054.483798] Model parameter optimization (eps = 1.000000) [09:04:07 -121019.761960] SLOW spr round 1 (radius: 5) [09:05:27 -120987.028430] SLOW spr round 2 (radius: 5) [09:06:47 -120977.284093] SLOW spr round 3 (radius: 5) [09:08:06 -120974.913301] SLOW spr round 4 (radius: 5) [09:09:24 -120974.913126] SLOW spr round 5 (radius: 10) [09:10:46 -120972.739559] SLOW spr round 6 (radius: 5) [09:12:17 -120972.739015] SLOW spr round 7 (radius: 10) [09:13:44 -120972.738946] SLOW spr round 8 (radius: 15) [09:15:28 -120972.612523] SLOW spr round 9 (radius: 5) [09:17:05 -120972.612520] SLOW spr round 10 (radius: 10) [09:18:36 -120972.612518] SLOW spr round 11 (radius: 15) [09:20:19 -120972.612517] SLOW spr round 12 (radius: 20) [09:23:01 -120972.267721] SLOW spr round 13 (radius: 5) [09:24:40 -120968.125700] SLOW spr round 14 (radius: 5) [09:26:08 -120968.125543] SLOW spr round 15 (radius: 10) [09:27:34 -120968.125542] SLOW spr round 16 (radius: 15) [09:29:20 -120968.125541] SLOW spr round 17 (radius: 20) [09:31:57 -120968.125540] SLOW spr round 18 (radius: 25) [09:35:22 -120968.125539] Model parameter optimization (eps = 0.100000) [09:35:29] ML tree search #17, logLikelihood: -120967.780207 [09:35:29 -810762.726846] Initial branch length optimization [09:35:31 -633074.108376] Model parameter optimization (eps = 10.000000) [09:35:49 -632576.249524] AUTODETECT spr round 1 (radius: 5) [09:37:20 -363735.169902] AUTODETECT spr round 2 (radius: 10) [09:38:53 -234676.161684] AUTODETECT spr round 3 (radius: 15) [09:40:28 -185836.910326] AUTODETECT spr round 4 (radius: 20) [09:42:17 -172479.650781] AUTODETECT spr round 5 (radius: 25) [09:44:10 -162318.992080] SPR radius for FAST iterations: 25 (autodetect) [09:44:10 -162318.992080] Model parameter optimization (eps = 3.000000) [09:44:29 -162055.860068] FAST spr round 1 (radius: 25) [09:46:05 -129445.493330] FAST spr round 2 (radius: 25) [09:47:23 -121767.499097] FAST spr round 3 (radius: 25) [09:48:34 -121056.617497] FAST spr round 4 (radius: 25) [09:49:46 -121016.362260] FAST spr round 5 (radius: 25) [09:50:52 -121006.278522] FAST spr round 6 (radius: 25) [09:51:58 -121006.277454] Model parameter optimization (eps = 1.000000) [09:52:09 -120987.458131] SLOW spr round 1 (radius: 5) [09:53:28 -120967.489819] SLOW spr round 2 (radius: 5) [09:54:45 -120967.487897] SLOW spr round 3 (radius: 10) [09:56:08 -120967.487647] SLOW spr round 4 (radius: 15) [09:57:59 -120967.487619] SLOW spr round 5 (radius: 20) [10:00:46 -120967.487615] SLOW spr round 6 (radius: 25) [10:04:16 -120967.487613] Model parameter optimization (eps = 0.100000) [10:04:22] ML tree search #18, logLikelihood: -120967.267767 [10:04:22 -811627.354046] Initial branch length optimization [10:04:25 -632330.631229] Model parameter optimization (eps = 10.000000) [10:04:49 -631743.171162] AUTODETECT spr round 1 (radius: 5) [10:06:21 -367303.628789] AUTODETECT spr round 2 (radius: 10) [10:07:54 -234317.957615] AUTODETECT spr round 3 (radius: 15) [10:09:34 -181103.690290] AUTODETECT spr round 4 (radius: 20) [10:11:25 -157470.741120] AUTODETECT spr round 5 (radius: 25) [10:13:12 -143264.284202] SPR radius for FAST iterations: 25 (autodetect) [10:13:12 -143264.284202] Model parameter optimization (eps = 3.000000) [10:13:32 -143103.397835] FAST spr round 1 (radius: 25) [10:15:09 -124022.046106] FAST spr round 2 (radius: 25) [10:16:26 -121521.593529] FAST spr round 3 (radius: 25) [10:17:38 -121047.107358] FAST spr round 4 (radius: 25) [10:18:47 -121035.464860] FAST spr round 5 (radius: 25) [10:19:55 -121022.557652] FAST spr round 6 (radius: 25) [10:21:00 -121022.557121] Model parameter optimization (eps = 1.000000) [10:21:09 -121016.740842] SLOW spr round 1 (radius: 5) [10:22:27 -120975.687892] SLOW spr round 2 (radius: 5) [10:23:47 -120970.565616] SLOW spr round 3 (radius: 5) [10:25:07 -120968.426883] SLOW spr round 4 (radius: 5) [10:26:26 -120968.426290] SLOW spr round 5 (radius: 10) [10:27:49 -120968.426096] SLOW spr round 6 (radius: 15) [10:29:38 -120968.425920] SLOW spr round 7 (radius: 20) [10:32:08 -120968.425919] SLOW spr round 8 (radius: 25) [10:35:17 -120968.425919] Model parameter optimization (eps = 0.100000) [10:35:24] ML tree search #19, logLikelihood: -120968.239973 [10:35:24 -813211.257632] Initial branch length optimization [10:35:27 -636388.334143] Model parameter optimization (eps = 10.000000) [10:35:47 -635782.844720] AUTODETECT spr round 1 (radius: 5) [10:37:17 -369453.517761] AUTODETECT spr round 2 (radius: 10) [10:38:52 -234655.066625] AUTODETECT spr round 3 (radius: 15) [10:40:31 -176323.108618] AUTODETECT spr round 4 (radius: 20) [10:42:15 -151559.255828] AUTODETECT spr round 5 (radius: 25) [10:44:03 -139983.930082] SPR radius for FAST iterations: 25 (autodetect) [10:44:03 -139983.930082] Model parameter optimization (eps = 3.000000) [10:44:20 -139784.983412] FAST spr round 1 (radius: 25) [10:45:51 -122344.307972] FAST spr round 2 (radius: 25) [10:47:07 -121171.883690] FAST spr round 3 (radius: 25) [10:48:20 -121042.710375] FAST spr round 4 (radius: 25) [10:49:27 -121039.818093] FAST spr round 5 (radius: 25) [10:50:32 -121039.818055] Model parameter optimization (eps = 1.000000) [10:50:43 -121024.049015] SLOW spr round 1 (radius: 5) [10:52:02 -120996.141323] SLOW spr round 2 (radius: 5) [10:53:22 -120988.622753] SLOW spr round 3 (radius: 5) [10:54:41 -120988.622315] SLOW spr round 4 (radius: 10) [10:56:05 -120988.380637] SLOW spr round 5 (radius: 5) [10:57:38 -120988.380550] SLOW spr round 6 (radius: 10) [10:59:08 -120988.380550] SLOW spr round 7 (radius: 15) [11:00:55 -120988.380550] SLOW spr round 8 (radius: 20) [11:03:40 -120988.380549] SLOW spr round 9 (radius: 25) [11:07:08 -120988.380549] Model parameter optimization (eps = 0.100000) [11:07:15] ML tree search #20, logLikelihood: -120988.067613 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.191225,0.417159) (0.278335,0.544423) (0.347529,1.124258) (0.182911,2.066496) Base frequencies (model): M0: 0.147383 0.017579 0.058208 0.017707 0.026331 0.041582 0.017494 0.027859 0.011849 0.076971 0.147823 0.019535 0.037132 0.029940 0.008059 0.088179 0.089653 0.006477 0.032308 0.097931 M1: 0.063139 0.066357 0.011586 0.066571 0.010800 0.009276 0.053984 0.146986 0.034214 0.088822 0.098196 0.032390 0.021263 0.072697 0.016761 0.020711 0.020797 0.025463 0.045615 0.094372 M2: 0.062457 0.066826 0.049332 0.065270 0.006513 0.041231 0.058965 0.080852 0.028024 0.037024 0.075925 0.064131 0.019620 0.028710 0.104579 0.056388 0.062027 0.008241 0.033124 0.050760 M3: 0.106471 0.074171 0.044513 0.096390 0.002148 0.066733 0.158908 0.037625 0.020691 0.014608 0.028797 0.105352 0.007864 0.007477 0.083595 0.055726 0.047711 0.003975 0.010088 0.027159 Substitution rates (model): M 0: 0.295719 0.067388 0.253712 1.029289 0.107964 0.514644 10.868848 0.380498 0.084223 0.086976 0.188789 0.286389 0.155567 1.671061 2.132922 0.529591 0.115551 0.102453 0.916683 0.448317 0.457483 0.576016 1.741924 0.736017 0.704334 5.658311 0.123387 0.221777 93.433377 0.382175 0.235965 6.535048 0.525521 0.303537 0.641259 0.289466 0.102065 2.358429 0.251987 0.216561 0.503084 0.435271 4.873453 0.090748 0.033310 0.746537 0.128905 0.127321 0.904011 0.939733 0.435450 0.046646 0.262076 0.043986 0.189008 0.599450 109.901504 1.070052 5.229858 0.052764 0.021407 0.621146 0.081091 0.205164 5.164456 0.747330 0.308078 0.260889 0.185083 0.080708 0.029955 0.084794 1.862626 0.553477 0.151733 0.230320 0.096955 0.352526 0.590018 0.386853 1.559564 0.606648 0.587531 0.592318 0.885230 4.117654 0.246260 6.508329 0.054187 0.195703 1.669092 0.810168 0.066081 2.437439 0.165666 0.106333 0.093417 0.035149 0.072549 1.202023 1.634845 0.060194 0.069359 2.448827 0.232297 0.064822 3.537387 0.435384 0.290413 0.280695 0.105999 0.206603 0.404968 0.048984 0.069963 0.256662 0.228519 0.241077 4.320442 3.656545 0.290216 0.307466 0.096556 0.306067 0.204296 0.504221 1.991533 0.655465 6.799829 11.291065 0.961142 0.448965 6.227274 20.304886 0.205944 1.495537 0.091940 1.994320 0.754940 0.170343 0.050315 0.372166 0.206332 0.097050 5.381403 0.122332 3.256485 2.261319 0.848067 0.064441 0.102493 0.459041 0.133091 0.561215 0.457430 0.163849 5.260446 0.360946 0.389413 0.033291 0.115301 0.112593 1.559944 0.426508 0.132547 0.498634 0.559069 0.264728 0.693307 0.438856 0.306683 0.109129 18.392863 66.647302 0.400021 4.586081 2.099355 0.411347 0.476350 0.584622 3.634276 0.101797 0.148995 0.089177 0.034710 0.063603 0.755865 20.561407 0.133790 0.154902 M 1: 0.066142 0.590377 0.069930 9.850951 1.101363 0.150375 0.568586 0.051668 0.127170 0.292429 0.071458 1.218562 0.075144 7.169085 30.139501 13.461692 0.021372 0.045779 4.270235 0.468325 0.013688 0.302287 1.353957 0.028386 0.037750 0.262130 0.016923 0.064289 0.855973 0.079621 0.011169 0.161937 0.276530 0.161053 0.081472 0.036742 0.030342 2.851667 3.932151 8.159169 0.219934 0.421974 2.468752 0.344765 0.210724 1.172204 0.763553 0.082464 0.726566 11.149790 4.782635 0.058046 0.498072 0.258487 0.146882 0.249672 0.560142 0.046719 0.106259 0.003656 0.004200 0.014189 0.009876 0.002656 0.040244 0.267322 0.053740 0.006597 0.027639 0.012745 0.582670 0.005035 0.275844 0.098208 0.445038 1.217010 0.033969 1.988516 0.681161 0.825960 18.762977 11.949233 0.286794 0.534219 4.336817 3.054085 0.129551 4.210126 0.165753 1.088704 1.889645 3.344809 0.111063 2.067758 3.547017 2.466507 0.188236 0.203493 0.281953 0.037250 0.029788 0.008541 0.014768 0.125869 0.056702 0.004186 0.110993 0.201148 0.139705 0.009201 0.012095 0.043812 0.013513 0.002533 0.005848 0.031390 0.021612 0.004854 0.129497 0.976631 0.053397 0.019475 0.004964 0.015539 0.031779 0.064558 0.065585 0.079927 0.095591 0.196886 0.408834 0.126088 0.037226 0.452302 0.016212 7.278994 0.029917 7.918203 0.450964 0.169797 0.104288 1.578530 0.015909 0.094365 16.179952 0.042762 14.799537 1.506485 0.637893 0.123793 0.641351 0.154810 0.140750 3.416059 0.259400 0.009457 0.090576 0.292108 0.297913 0.017172 0.021976 0.032578 1.375871 0.457399 0.598048 4.418398 0.239749 0.168432 2.950318 0.143327 0.328689 0.125011 0.562720 1.414883 0.227807 3.478333 2.984862 0.061299 0.077470 1.050562 13.974326 0.154326 0.224675 0.112000 0.060703 0.123480 5.294490 0.447011 0.033381 0.045528 M 2: 0.733336 0.558955 0.503360 4.149599 1.415369 1.367574 1.263002 0.994098 0.517204 0.775054 0.763094 1.890137 0.540460 0.200122 4.972745 1.825593 0.450842 0.526135 3.839269 0.597671 0.058964 2.863355 2.872594 0.258365 0.366868 2.578946 0.358350 0.672023 5.349861 0.691594 0.063347 0.032875 0.821562 0.580847 0.661866 0.265730 0.395134 5.581680 1.279881 1.335650 0.397108 1.840061 5.739035 0.284730 0.109781 1.612642 0.466979 0.141582 0.019509 4.670980 1.967383 0.088064 0.581928 0.145401 0.225860 0.434096 2.292917 1.024707 0.821921 0.027824 0.021443 0.088850 0.060820 0.018288 0.042687 1.199607 0.420710 0.037642 0.141233 0.090101 1.043232 0.209978 0.823594 3.039380 1.463390 1.983693 0.397640 2.831098 4.102068 0.059723 5.901348 2.034980 2.600668 5.413080 4.193725 4.534772 0.377181 4.877840 0.370939 1.298542 3.509873 2.646440 0.087872 0.072299 1.139018 0.864479 0.390688 0.322761 0.625409 0.496780 0.532488 0.232460 0.169219 0.755219 0.379926 0.020447 0.023282 0.503875 0.577513 0.109318 0.153776 0.696533 0.398817 0.008940 0.043707 0.436013 0.087640 0.064863 0.036426 1.673207 0.124068 0.218118 0.039217 0.104335 0.349195 0.838324 0.888693 0.488389 1.385133 0.050226 0.962470 0.502294 1.065585 8.351808 0.377304 5.102837 0.561690 7.010411 3.054968 0.039318 0.204155 2.653232 0.564368 0.854294 15.559906 0.401070 8.929538 5.525874 0.067505 0.273372 0.437116 1.927515 0.940458 2.508169 1.357738 0.043394 0.023126 0.567639 1.048288 0.120994 0.180650 0.449074 3.135353 0.012695 0.570771 2.319555 1.856122 0.975427 3.404087 0.015631 0.458799 0.151684 4.154750 11.429924 1.457957 0.233109 0.077004 0.011074 0.026268 0.052132 8.113282 0.377578 0.429221 0.260296 0.222293 0.273138 2.903836 4.731579 0.564762 0.681215 M 3: 0.658412 0.566269 0.854111 0.884454 1.309554 1.272639 1.874713 0.552007 0.227683 0.581512 0.695190 0.967985 0.344015 0.978992 3.427163 2.333253 0.154701 0.221089 2.088785 0.540749 0.058015 5.851132 2.294145 0.182966 0.684164 3.192521 0.528161 1.128882 3.010922 1.012866 0.227296 0.156635 0.878405 0.802754 0.830884 0.431617 0.456530 3.060574 1.279257 1.438430 0.431464 2.075952 4.840271 0.644656 0.266076 2.084975 0.720060 0.291854 0.028961 4.071574 2.258357 0.073037 1.238426 0.199728 0.160296 0.482619 2.992763 1.296206 0.841829 0.031467 0.048542 0.132774 0.133055 0.056045 0.209188 0.925172 0.360522 0.094591 0.313945 0.118104 0.992259 0.086318 2.149634 5.103188 3.775817 3.954021 0.190734 1.776095 4.495841 0.264277 7.063879 2.221150 3.017954 8.558815 4.310199 2.130054 0.571406 4.137385 0.437589 2.071689 2.498630 1.763546 0.116381 0.296578 1.033710 1.283423 0.312579 0.305772 0.681277 0.507160 0.351381 0.189152 0.217780 0.767361 0.278392 0.092075 0.177263 0.451893 0.653836 0.074620 0.181992 0.752277 0.679853 0.025780 0.082005 0.326441 0.343977 0.195877 0.217424 3.057583 0.377558 0.401252 0.072258 0.241015 0.665865 1.266791 0.680174 0.717301 4.001286 0.362942 1.189259 0.964545 1.350568 12.869737 0.531100 8.904999 0.652629 10.091413 2.671718 0.086367 0.359932 4.797423 0.336801 1.021885 23.029406 0.440178 14.013035 5.069337 0.539010 0.742569 0.780580 1.331875 1.531589 4.414850 1.082703 0.091278 0.172734 0.693405 1.422571 0.068958 0.163829 0.481711 4.643214 0.121821 0.584083 4.216178 1.677263 1.575754 5.046403 0.161015 1.531223 0.599244 5.832025 33.873091 1.914768 1.287474 0.444362 0.076328 0.079916 0.466823 5.231362 0.548763 0.831890 0.382271 0.208791 0.307846 3.717971 5.910440 0.282540 0.964421 Final LogLikelihood: -120939.844373 AIC score: 245889.688745 / AICc score: 8289949.688745 / BIC score: 254497.994399 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=541). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 329 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08575/3_mltree/P08575.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08575/3_mltree/P08575.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08575/3_mltree/P08575.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08575/3_mltree/P08575.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08575/3_mltree/P08575.raxml.log Analysis started: 02-Jul-2021 09:42:45 / finished: 02-Jul-2021 20:50:01 Elapsed time: 40036.039 seconds Consumed energy: 3702.877 Wh (= 19 km in an electric car, or 93 km with an e-scooter!)