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 05-Jul-2021 00:12:38 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQM7/2_msa/Q9UQM7_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQM7/3_mltree/Q9UQM7 --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/Q9UQM7/2_msa/Q9UQM7_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 495 sites

WARNING: Sequences sp_O70589_CSKP_MOUSE_10090 and tr_A0A2I2ZHQ2_A0A2I2ZHQ2_GORGO_9595 are exactly identical!
WARNING: Sequences sp_O70589_CSKP_MOUSE_10090 and tr_G1SMP3_G1SMP3_RABIT_9986 are exactly identical!
WARNING: Sequences sp_O70589_CSKP_MOUSE_10090 and sp_O14936_CSKP_HUMAN_9606 are exactly identical!
WARNING: Sequences sp_O70589_CSKP_MOUSE_10090 and tr_A0A1D5QVF6_A0A1D5QVF6_MACMU_9544 are exactly identical!
WARNING: Sequences sp_O70589_CSKP_MOUSE_10090 and tr_G3SZ61_G3SZ61_LOXAF_9785 are exactly identical!
WARNING: Sequences sp_O70589_CSKP_MOUSE_10090 and tr_U3CM89_U3CM89_CALJA_9483 are exactly identical!
WARNING: Sequences sp_O70589_CSKP_MOUSE_10090 and tr_G1LJM6_G1LJM6_AILME_9646 are exactly identical!
WARNING: Sequences sp_O70589_CSKP_MOUSE_10090 and tr_A5D7B9_A5D7B9_BOVIN_9913 are exactly identical!
WARNING: Sequences sp_O70589_CSKP_MOUSE_10090 and tr_A0A1S2ZLD9_A0A1S2ZLD9_ERIEU_9365 are exactly identical!
WARNING: Sequences sp_O70589_CSKP_MOUSE_10090 and tr_A0A1S3GBV8_A0A1S3GBV8_DIPOR_10020 are exactly identical!
WARNING: Sequences sp_O70589_CSKP_MOUSE_10090 and tr_A0A2K5P101_A0A2K5P101_CERAT_9531 are exactly identical!
WARNING: Sequences sp_O70589_CSKP_MOUSE_10090 and tr_A0A2K5YGA4_A0A2K5YGA4_MANLE_9568 are exactly identical!
WARNING: Sequences sp_O70589_CSKP_MOUSE_10090 and tr_A0A2R9C8L1_A0A2R9C8L1_PANPA_9597 are exactly identical!
WARNING: Sequences sp_P11798_KCC2A_MOUSE_10090 and tr_F1PB67_F1PB67_CANLF_9615 are exactly identical!
WARNING: Sequences sp_P11798_KCC2A_MOUSE_10090 and tr_W5PAI9_W5PAI9_SHEEP_9940 are exactly identical!
WARNING: Sequences sp_P11798_KCC2A_MOUSE_10090 and sp_P11275_KCC2A_RAT_10116 are exactly identical!
WARNING: Sequences sp_P11798_KCC2A_MOUSE_10090 and tr_Q08E45_Q08E45_BOVIN_9913 are exactly identical!
WARNING: Sequences sp_Q6PHZ2_KCC2D_MOUSE_10090 and tr_F6PTM3_F6PTM3_HORSE_9796 are exactly identical!
WARNING: Sequences sp_Q6PHZ2_KCC2D_MOUSE_10090 and sp_Q13557_KCC2D_HUMAN_9606 are exactly identical!
WARNING: Sequences sp_Q6PHZ2_KCC2D_MOUSE_10090 and sp_Q95266_KCC2D_PIG_9823 are exactly identical!
WARNING: Sequences sp_Q6PHZ2_KCC2D_MOUSE_10090 and tr_G1LRM2_G1LRM2_AILME_9646 are exactly identical!
WARNING: Sequences sp_Q6PHZ2_KCC2D_MOUSE_10090 and tr_G7P650_G7P650_MACFA_9541 are exactly identical!
WARNING: Sequences sp_Q6PHZ2_KCC2D_MOUSE_10090 and tr_A0A1S3FSD2_A0A1S3FSD2_DIPOR_10020 are exactly identical!
WARNING: Sequences sp_Q923T9_KCC2G_MOUSE_10090 and tr_E2RG56_E2RG56_CANLF_9615 are exactly identical!
WARNING: Sequences tr_M3YA76_M3YA76_MUSPF_9669 and tr_W5QAM4_W5QAM4_SHEEP_9940 are exactly identical!
WARNING: Sequences tr_M3YA76_M3YA76_MUSPF_9669 and tr_F6UGY3_F6UGY3_MACMU_9544 are exactly identical!
WARNING: Sequences tr_M3YMI8_M3YMI8_MUSPF_9669 and tr_A0A2I2UBK1_A0A2I2UBK1_FELCA_9685 are exactly identical!
WARNING: Sequences sp_Q00168_KCC2A_DROME_7227 and tr_B4IKQ9_B4IKQ9_DROSE_7238 are exactly identical!
WARNING: Sequences tr_B4JZN8_B4JZN8_DROGR_7222 and tr_D0Z795_D0Z795_DROVI_7244 are exactly identical!
WARNING: Sequences tr_B4JZN8_B4JZN8_DROGR_7222 and tr_A0A0Q9XG85_A0A0Q9XG85_DROMO_7230 are exactly identical!
WARNING: Sequences tr_B4JZN8_B4JZN8_DROGR_7222 and tr_A0A0M5J0P2_A0A0M5J0P2_DROBS_30019 are exactly identical!
WARNING: Sequences tr_A0A2I3H8G5_A0A2I3H8G5_NOMLE_61853 and tr_G3S8D3_G3S8D3_GORGO_9595 are exactly identical!
WARNING: Sequences tr_A0A2I3H8G5_A0A2I3H8G5_NOMLE_61853 and tr_F7H6F9_F7H6F9_CALJA_9483 are exactly identical!
WARNING: Sequences tr_A0A2I3H8G5_A0A2I3H8G5_NOMLE_61853 and tr_A0A337S4F5_A0A337S4F5_FELCA_9685 are exactly identical!
WARNING: Sequences tr_A0A2I3H8G5_A0A2I3H8G5_NOMLE_61853 and tr_A0A2I3NFL1_A0A2I3NFL1_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I3H8G5_A0A2I3H8G5_NOMLE_61853 and tr_A0A2K5MKI0_A0A2K5MKI0_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3H8G5_A0A2I3H8G5_NOMLE_61853 and tr_A0A2K6ED16_A0A2K6ED16_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3H8G5_A0A2I3H8G5_NOMLE_61853 and tr_A0A2R9AEX7_A0A2R9AEX7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3H8G5_A0A2I3H8G5_NOMLE_61853 and tr_A0A2Y9K9I9_A0A2Y9K9I9_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A2I2Y6I6_A0A2I2Y6I6_GORGO_9595 and tr_H2PH29_H2PH29_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I2Y6I6_A0A2I2Y6I6_GORGO_9595 and tr_A0A2I3STB7_A0A2I3STB7_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2Y6I6_A0A2I2Y6I6_GORGO_9595 and tr_U3E1F8_U3E1F8_CALJA_9483 are exactly identical!
WARNING: Sequences tr_A0A2I2Y6I6_A0A2I2Y6I6_GORGO_9595 and tr_A0A096N2J8_A0A096N2J8_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I2Y6I6_A0A2I2Y6I6_GORGO_9595 and tr_A0A2K5MDN6_A0A2K5MDN6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I2Y6I6_A0A2I2Y6I6_GORGO_9595 and tr_A0A2K6E5G5_A0A2K6E5G5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I2Y6I6_A0A2I2Y6I6_GORGO_9595 and tr_A0A2K5ZWB6_A0A2K5ZWB6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I2Y6I6_A0A2I2Y6I6_GORGO_9595 and tr_A0A2R9CAT1_A0A2R9CAT1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I2YEC7_A0A2I2YEC7_GORGO_9595 and tr_A0A2R9ARJ0_A0A2R9ARJ0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3RK85_G3RK85_GORGO_9595 and tr_H2N9S4_H2N9S4_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3RK85_G3RK85_GORGO_9595 and tr_H2Q1M3_H2Q1M3_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RK85_G3RK85_GORGO_9595 and sp_Q8IU85_KCC1D_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3RK85_G3RK85_GORGO_9595 and tr_H9FXH1_H9FXH1_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G3RK85_G3RK85_GORGO_9595 and tr_A0A2K5LSL0_A0A2K5LSL0_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G3RK85_G3RK85_GORGO_9595 and tr_A0A2K6DCE4_A0A2K6DCE4_MACNE_9545 are exactly identical!
WARNING: Sequences sp_Q5RCC4_KCC2A_PONAB_9601 and sp_Q9UQM7_KCC2A_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_Q29CP9_Q29CP9_DROPS_46245 and tr_B4H883_B4H883_DROPE_7234 are exactly identical!
WARNING: Sequences tr_A0A2I3S8G4_A0A2I3S8G4_PANTR_9598 and sp_Q13554_KCC2B_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3S8G4_A0A2I3S8G4_PANTR_9598 and tr_F7CW72_F7CW72_CALJA_9483 are exactly identical!
WARNING: Sequences tr_A0A2I3S8G4_A0A2I3S8G4_PANTR_9598 and tr_A0A2I3NG95_A0A2I3NG95_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I3S8G4_A0A2I3S8G4_PANTR_9598 and tr_A0A0D9RSU7_A0A0D9RSU7_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I3S8G4_A0A2I3S8G4_PANTR_9598 and tr_A0A2K5M5C4_A0A2K5M5C4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3S8G4_A0A2I3S8G4_PANTR_9598 and tr_A0A2K6D7W8_A0A2K6D7W8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H2R4R8_H2R4R8_PANTR_9598 and sp_Q62915_CSKP_RAT_10116 are exactly identical!
WARNING: Sequences tr_F6TEC0_F6TEC0_HORSE_9796 and sp_Q13555_KCC2G_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_F6TEC0_F6TEC0_HORSE_9796 and tr_A0A286ZKT1_A0A286ZKT1_PIG_9823 are exactly identical!
WARNING: Sequences tr_F6TEC0_F6TEC0_HORSE_9796 and tr_A0A2I2U9U9_A0A2I2U9U9_FELCA_9685 are exactly identical!
WARNING: Sequences tr_F6TEC0_F6TEC0_HORSE_9796 and tr_A0A096P4K7_A0A096P4K7_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6TEC0_F6TEC0_HORSE_9796 and tr_A0A0D9R9D2_A0A0D9R9D2_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_F6TEC0_F6TEC0_HORSE_9796 and tr_A0A1S3W7V0_A0A1S3W7V0_ERIEU_9365 are exactly identical!
WARNING: Sequences tr_F6TEC0_F6TEC0_HORSE_9796 and tr_A0A2K5NKH4_A0A2K5NKH4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F6TEC0_F6TEC0_HORSE_9796 and tr_A0A2Y9J612_A0A2Y9J612_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_F7CJA9_F7CJA9_HORSE_9796 and tr_H0WQA2_H0WQA2_OTOGA_30611 are exactly identical!
WARNING: Sequences tr_F7CJA9_F7CJA9_HORSE_9796 and tr_G5C394_G5C394_HETGA_10181 are exactly identical!
WARNING: Sequences tr_F7CJA9_F7CJA9_HORSE_9796 and tr_L5L0V1_L5L0V1_PTEAL_9402 are exactly identical!
WARNING: Sequences tr_F7CJA9_F7CJA9_HORSE_9796 and tr_A0A1S3FWM4_A0A1S3FWM4_DIPOR_10020 are exactly identical!
WARNING: Sequences tr_F7CJA9_F7CJA9_HORSE_9796 and tr_A0A2U3W4A5_A0A2U3W4A5_ODORO_9708 are exactly identical!
WARNING: Sequences tr_I3LWN4_I3LWN4_ICTTR_43179 and tr_A0A1U7R3L0_A0A1U7R3L0_MESAU_10036 are exactly identical!
WARNING: Sequences tr_I3MCL2_I3MCL2_ICTTR_43179 and tr_H0V888_H0V888_CAVPO_10141 are exactly identical!
WARNING: Sequences tr_I3MCL2_I3MCL2_ICTTR_43179 and tr_F1RL74_F1RL74_PIG_9823 are exactly identical!
WARNING: Sequences tr_I3MCL2_I3MCL2_ICTTR_43179 and tr_M3W0P7_M3W0P7_FELCA_9685 are exactly identical!
WARNING: Sequences tr_I3MCL2_I3MCL2_ICTTR_43179 and tr_A0A1S2ZAN5_A0A1S2ZAN5_ERIEU_9365 are exactly identical!
WARNING: Sequences tr_I3MCL2_I3MCL2_ICTTR_43179 and tr_A0A3Q0E287_A0A3Q0E287_TARSY_1868482 are exactly identical!
WARNING: Sequences tr_I3MCL2_I3MCL2_ICTTR_43179 and tr_A0A2Y9IKI9_A0A2Y9IKI9_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G0NFY5_G0NFY5_CAEBE_135651 and tr_G0P8Y9_G0P8Y9_CAEBE_135651 are exactly identical!
WARNING: Sequences tr_W2QYX2_W2QYX2_PHYPN_761204 and tr_A0A0W8BK56_A0A0W8BK56_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2QYX2_W2QYX2_PHYPN_761204 and tr_W2I6Z9_W2I6Z9_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W2RD06_W2RD06_PHYPN_761204 and tr_A0A0W8D224_A0A0W8D224_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2RD06_W2RD06_PHYPN_761204 and tr_W2J829_W2J829_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A015JR60_A0A015JR60_9GLOM_1432141 and tr_A0A2H5T156_A0A2H5T156_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A2I3LXC9_A0A2I3LXC9_PAPAN_9555 and tr_A0A2K6D560_A0A2K6D560_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A151M7C2_A0A151M7C2_ALLMI_8496 and tr_A0A1U7RYB9_A0A1U7RYB9_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A0W8C5Z3_A0A0W8C5Z3_PHYNI_4790 and tr_W2JWL5_W2JWL5_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A0W8DQ77_A0A0W8DQ77_PHYNI_4790 and tr_W2GJQ0_W2GJQ0_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A091IW34_A0A091IW34_EGRGA_188379 and tr_A0A093Q1H6_A0A093Q1H6_9PASS_328815 are exactly identical!
WARNING: Sequences tr_A0A091IW34_A0A091IW34_EGRGA_188379 and tr_A0A091V724_A0A091V724_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091IW34_A0A091IW34_EGRGA_188379 and tr_A0A087RE42_A0A087RE42_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091IW34_A0A091IW34_EGRGA_188379 and tr_A0A091WSD8_A0A091WSD8_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A091IW34_A0A091IW34_EGRGA_188379 and tr_A0A099ZB55_A0A099ZB55_TINGU_94827 are exactly identical!
WARNING: Sequences tr_A0A091FIZ0_A0A091FIZ0_9AVES_55661 and tr_A0A0A0ADQ5_A0A0A0ADQ5_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A2I0MH53_A0A2I0MH53_COLLI_8932 and tr_A0A1V4K061_A0A1V4K061_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A0V0RL84_A0A0V0RL84_9BILA_6336 and tr_A0A0V1A9G1_A0A0V1A9G1_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A0V1D7J2_A0A0V1D7J2_TRIBR_45882 and tr_A0A0V0VI16_A0A0V0VI16_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1D7J2_A0A0V1D7J2_TRIBR_45882 and tr_A0A0V1NUL9_A0A0V1NUL9_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V1D7J2_A0A0V1D7J2_TRIBR_45882 and tr_A0A0V0TJP0_A0A0V0TJP0_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V0XA41_A0A0V0XA41_9BILA_92179 and tr_A0A0V1L2Q3_A0A0V1L2Q3_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V0XA41_A0A0V0XA41_9BILA_92179 and tr_A0A0V0ZND3_A0A0V0ZND3_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A0V0VEZ6_A0A0V0VEZ6_9BILA_181606 and tr_A0A0V0TWQ8_A0A0V0TWQ8_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V1MA43_A0A0V1MA43_9BILA_268474 and tr_A0A0V1HWB8_A0A0V1HWB8_9BILA_268475 are exactly identical!
WARNING: Sequences tr_A0A1J1IPH7_A0A1J1IPH7_9DIPT_568069 and tr_A0A1J1IUB9_A0A1J1IUB9_9DIPT_568069 are exactly identical!
WARNING: Sequences tr_A0A226MWP9_A0A226MWP9_CALSU_9009 and tr_A0A226P8W8_A0A226P8W8_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0QMU5_A0A2D0QMU5_ICTPU_7998 and tr_A0A2D0QQ22_A0A2D0QQ22_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QMV4_A0A2D0QMV4_ICTPU_7998 and tr_A0A2D0QN59_A0A2D0QN59_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0S825_A0A2D0S825_ICTPU_7998 and tr_A0A2D0S8Y4_A0A2D0S8Y4_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0S826_A0A2D0S826_ICTPU_7998 and tr_A0A2D0S843_A0A2D0S843_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0S830_A0A2D0S830_ICTPU_7998 and tr_A0A2D0S8Y6_A0A2D0S8Y6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0S832_A0A2D0S832_ICTPU_7998 and tr_A0A2D0S8Z1_A0A2D0S8Z1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0S835_A0A2D0S835_ICTPU_7998 and tr_A0A2D0S847_A0A2D0S847_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SQA9_A0A2D0SQA9_ICTPU_7998 and tr_A0A2D0SQB8_A0A2D0SQB8_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SQA9_A0A2D0SQA9_ICTPU_7998 and tr_A0A2D0SQC5_A0A2D0SQC5_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SQA9_A0A2D0SQA9_ICTPU_7998 and tr_A0A2D0SRI3_A0A2D0SRI3_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SQB6_A0A2D0SQB6_ICTPU_7998 and tr_A0A2D0SQC0_A0A2D0SQC0_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SQB6_A0A2D0SQB6_ICTPU_7998 and tr_A0A2D0SQW6_A0A2D0SQW6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SQB6_A0A2D0SQB6_ICTPU_7998 and tr_A0A2D0SQX7_A0A2D0SQX7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SQB6_A0A2D0SQB6_ICTPU_7998 and tr_W5UQH7_W5UQH7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SQB7_A0A2D0SQB7_ICTPU_7998 and tr_A0A2D0SQC1_A0A2D0SQC1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SQC6_A0A2D0SQC6_ICTPU_7998 and tr_A0A2D0SQD4_A0A2D0SQD4_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SQD1_A0A2D0SQD1_ICTPU_7998 and tr_A0A2D0SQY2_A0A2D0SQY2_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SQD9_A0A2D0SQD9_ICTPU_7998 and tr_A0A2D0SQE1_A0A2D0SQE1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SQD9_A0A2D0SQD9_ICTPU_7998 and tr_A0A2D0SQY6_A0A2D0SQY6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SQD9_A0A2D0SQD9_ICTPU_7998 and tr_A0A2D0SRJ1_A0A2D0SRJ1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SQX1_A0A2D0SQX1_ICTPU_7998 and tr_A0A2D0SRH6_A0A2D0SRH6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U4C112_A0A2U4C112_TURTR_9739 and tr_A0A2Y9R2G8_A0A2Y9R2G8_TRIMA_127582 are exactly identical!
WARNING: Sequences tr_A0A2U4C112_A0A2U4C112_TURTR_9739 and tr_A0A2Y9LTT7_A0A2Y9LTT7_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U4C112_A0A2U4C112_TURTR_9739 and tr_A0A2Y9EJ11_A0A2Y9EJ11_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2Y9EVL3_A0A2Y9EVL3_PHYCD_9755 and tr_A0A384AND8_A0A384AND8_BALAS_310752 are exactly identical!
WARNING: Sequences tr_A0A2Y9T4S3_A0A2Y9T4S3_PHYCD_9755 and tr_A0A383YXR9_A0A383YXR9_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 136

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/Q9UQM7/3_mltree/Q9UQM7.raxml.reduced.phy

Alignment comprises 1 partitions and 495 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 495 / 495
Gaps: 17.44 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQM7/3_mltree/Q9UQM7.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 / 71 / 5680
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -573767.552348] Initial branch length optimization
[00:00:02 -433421.386738] Model parameter optimization (eps = 10.000000)
[00:00:31 -432073.916249] AUTODETECT spr round 1 (radius: 5)
[00:02:18 -281283.574031] AUTODETECT spr round 2 (radius: 10)
[00:04:14 -201389.450927] AUTODETECT spr round 3 (radius: 15)
[00:06:13 -181287.442341] AUTODETECT spr round 4 (radius: 20)
[00:08:24 -157450.470972] AUTODETECT spr round 5 (radius: 25)
[00:10:55 -151564.020981] SPR radius for FAST iterations: 25 (autodetect)
[00:10:55 -151564.020981] Model parameter optimization (eps = 3.000000)
[00:11:14 -151455.880698] FAST spr round 1 (radius: 25)
[00:13:30 -123596.921342] FAST spr round 2 (radius: 25)
[00:15:19 -120700.599767] FAST spr round 3 (radius: 25)
[00:16:59 -119777.170722] FAST spr round 4 (radius: 25)
[00:18:34 -119724.785542] FAST spr round 5 (radius: 25)
[00:20:06 -119713.247162] FAST spr round 6 (radius: 25)
[00:21:38 -119713.246314] Model parameter optimization (eps = 1.000000)
[00:21:55 -119699.351920] SLOW spr round 1 (radius: 5)
[00:23:47 -119667.056646] SLOW spr round 2 (radius: 5)
[00:25:37 -119658.562944] SLOW spr round 3 (radius: 5)
[00:27:26 -119657.538016] SLOW spr round 4 (radius: 5)
[00:29:13 -119657.536603] SLOW spr round 5 (radius: 10)
[00:31:03 -119656.763803] SLOW spr round 6 (radius: 5)
[00:33:10 -119656.739098] SLOW spr round 7 (radius: 10)
[00:35:11 -119656.738905] SLOW spr round 8 (radius: 15)
[00:37:39 -119656.322310] SLOW spr round 9 (radius: 5)
[00:39:50 -119656.320624] SLOW spr round 10 (radius: 10)
[00:41:56 -119656.320085] SLOW spr round 11 (radius: 15)
[00:44:23 -119656.319936] SLOW spr round 12 (radius: 20)
[00:47:36 -119654.925986] SLOW spr round 13 (radius: 5)
[00:49:49 -119654.925945] SLOW spr round 14 (radius: 10)
[00:51:57 -119654.925936] SLOW spr round 15 (radius: 15)
[00:54:22 -119654.925934] SLOW spr round 16 (radius: 20)
[00:57:34 -119654.925932] SLOW spr round 17 (radius: 25)
[01:01:38 -119651.991108] SLOW spr round 18 (radius: 5)
[01:03:53 -119651.963136] SLOW spr round 19 (radius: 10)
[01:06:01 -119651.548080] SLOW spr round 20 (radius: 5)
[01:08:03 -119651.539167] SLOW spr round 21 (radius: 10)
[01:10:01 -119650.628994] SLOW spr round 22 (radius: 5)
[01:12:06 -119648.414274] SLOW spr round 23 (radius: 5)
[01:14:02 -119647.252809] SLOW spr round 24 (radius: 5)
[01:15:50 -119647.252245] SLOW spr round 25 (radius: 10)
[01:17:39 -119647.252073] SLOW spr round 26 (radius: 15)
[01:20:10 -119647.252071] SLOW spr round 27 (radius: 20)
[01:23:15 -119647.252070] SLOW spr round 28 (radius: 25)
[01:26:57 -119647.252069] Model parameter optimization (eps = 0.100000)

[01:27:07] ML tree search #1, logLikelihood: -119646.768231

[01:27:07 -572032.677697] Initial branch length optimization
[01:27:09 -433099.065995] Model parameter optimization (eps = 10.000000)
[01:27:44 -431699.462217] AUTODETECT spr round 1 (radius: 5)
[01:29:23 -284174.898065] AUTODETECT spr round 2 (radius: 10)
[01:31:08 -212079.002176] AUTODETECT spr round 3 (radius: 15)
[01:32:58 -176983.410736] AUTODETECT spr round 4 (radius: 20)
[01:35:11 -155939.152058] AUTODETECT spr round 5 (radius: 25)
[01:37:45 -145419.412784] SPR radius for FAST iterations: 25 (autodetect)
[01:37:45 -145419.412784] Model parameter optimization (eps = 3.000000)
[01:38:08 -145218.481682] FAST spr round 1 (radius: 25)
[01:40:21 -121285.949830] FAST spr round 2 (radius: 25)
[01:42:03 -119747.064678] FAST spr round 3 (radius: 25)
[01:43:36 -119692.403823] FAST spr round 4 (radius: 25)
[01:45:07 -119680.873262] FAST spr round 5 (radius: 25)
[01:46:33 -119653.112847] FAST spr round 6 (radius: 25)
[01:47:59 -119649.635319] FAST spr round 7 (radius: 25)
[01:49:22 -119647.567908] FAST spr round 8 (radius: 25)
[01:50:46 -119646.087486] FAST spr round 9 (radius: 25)
[01:52:08 -119646.087382] Model parameter optimization (eps = 1.000000)
[01:52:21 -119640.040716] SLOW spr round 1 (radius: 5)
[01:54:01 -119615.726289] SLOW spr round 2 (radius: 5)
[01:55:40 -119615.724721] SLOW spr round 3 (radius: 10)
[01:57:22 -119615.357404] SLOW spr round 4 (radius: 5)
[01:59:19 -119614.001265] SLOW spr round 5 (radius: 5)
[02:01:05 -119614.000257] SLOW spr round 6 (radius: 10)
[02:02:48 -119614.000111] SLOW spr round 7 (radius: 15)
[02:05:06 -119613.995938] SLOW spr round 8 (radius: 20)
[02:08:02 -119612.650357] SLOW spr round 9 (radius: 5)
[02:10:03 -119612.650303] SLOW spr round 10 (radius: 10)
[02:11:57 -119612.650302] SLOW spr round 11 (radius: 15)
[02:14:09 -119612.650302] SLOW spr round 12 (radius: 20)
[02:17:03 -119612.650302] SLOW spr round 13 (radius: 25)
[02:20:32 -119612.647402] Model parameter optimization (eps = 0.100000)

[02:20:36] ML tree search #2, logLikelihood: -119612.605184

[02:20:37 -572983.121567] Initial branch length optimization
[02:20:39 -432790.974182] Model parameter optimization (eps = 10.000000)
[02:21:03 -431309.727673] AUTODETECT spr round 1 (radius: 5)
[02:22:42 -286729.231043] AUTODETECT spr round 2 (radius: 10)
[02:24:27 -218909.802118] AUTODETECT spr round 3 (radius: 15)
[02:26:17 -181440.299524] AUTODETECT spr round 4 (radius: 20)
[02:28:18 -169586.350808] AUTODETECT spr round 5 (radius: 25)
[02:30:37 -158383.901835] SPR radius for FAST iterations: 25 (autodetect)
[02:30:37 -158383.901835] Model parameter optimization (eps = 3.000000)
[02:30:56 -158146.937387] FAST spr round 1 (radius: 25)
[02:33:06 -130148.137244] FAST spr round 2 (radius: 25)
[02:34:53 -121009.999739] FAST spr round 3 (radius: 25)
[02:36:29 -119731.546846] FAST spr round 4 (radius: 25)
[02:37:59 -119675.620674] FAST spr round 5 (radius: 25)
[02:39:25 -119670.485330] FAST spr round 6 (radius: 25)
[02:40:49 -119670.484374] Model parameter optimization (eps = 1.000000)
[02:41:03 -119648.851892] SLOW spr round 1 (radius: 5)
[02:42:44 -119620.959359] SLOW spr round 2 (radius: 5)
[02:44:24 -119617.642486] SLOW spr round 3 (radius: 5)
[02:46:04 -119615.462845] SLOW spr round 4 (radius: 5)
[02:47:44 -119615.461803] SLOW spr round 5 (radius: 10)
[02:49:23 -119613.396223] SLOW spr round 6 (radius: 5)
[02:51:21 -119612.114596] SLOW spr round 7 (radius: 5)
[02:53:07 -119612.114092] SLOW spr round 8 (radius: 10)
[02:54:50 -119612.113714] SLOW spr round 9 (radius: 15)
[02:57:08 -119604.286354] SLOW spr round 10 (radius: 5)
[02:59:07 -119603.119713] SLOW spr round 11 (radius: 5)
[03:00:56 -119603.118826] SLOW spr round 12 (radius: 10)
[03:02:42 -119601.773059] SLOW spr round 13 (radius: 5)
[03:04:35 -119601.772978] SLOW spr round 14 (radius: 10)
[03:06:22 -119601.772847] SLOW spr round 15 (radius: 15)
[03:08:35 -119600.382264] SLOW spr round 16 (radius: 5)
[03:10:44 -119600.382198] SLOW spr round 17 (radius: 10)
[03:12:47 -119600.382151] SLOW spr round 18 (radius: 15)
[03:15:11 -119600.382151] SLOW spr round 19 (radius: 20)
[03:18:23 -119600.382151] SLOW spr round 20 (radius: 25)
[03:22:33 -119600.382150] Model parameter optimization (eps = 0.100000)

[03:22:43] ML tree search #3, logLikelihood: -119599.894216

[03:22:43 -569969.147973] Initial branch length optimization
[03:22:46 -430328.601915] Model parameter optimization (eps = 10.000000)
[03:23:12 -428975.993425] AUTODETECT spr round 1 (radius: 5)
[03:24:57 -288789.944075] AUTODETECT spr round 2 (radius: 10)
[03:26:54 -218799.976234] AUTODETECT spr round 3 (radius: 15)
[03:28:57 -174407.133272] AUTODETECT spr round 4 (radius: 20)
[03:31:20 -153584.807515] AUTODETECT spr round 5 (radius: 25)
[03:33:54 -143542.058187] SPR radius for FAST iterations: 25 (autodetect)
[03:33:54 -143542.058187] Model parameter optimization (eps = 3.000000)
[03:34:18 -143372.379860] FAST spr round 1 (radius: 25)
[03:36:36 -121223.646249] FAST spr round 2 (radius: 25)
[03:38:25 -119780.358673] FAST spr round 3 (radius: 25)
[03:40:07 -119688.378588] FAST spr round 4 (radius: 25)
[03:41:46 -119678.232088] FAST spr round 5 (radius: 25)
[03:43:21 -119677.951279] FAST spr round 6 (radius: 25)
[03:44:54 -119677.950486] Model parameter optimization (eps = 1.000000)
[03:45:05 -119677.146188] SLOW spr round 1 (radius: 5)
[03:46:57 -119653.896717] SLOW spr round 2 (radius: 5)
[03:48:47 -119650.959394] SLOW spr round 3 (radius: 5)
[03:50:34 -119650.959340] SLOW spr round 4 (radius: 10)
[03:52:26 -119650.958910] SLOW spr round 5 (radius: 15)
[03:55:01 -119650.958787] SLOW spr round 6 (radius: 20)
[03:58:11 -119649.637125] SLOW spr round 7 (radius: 5)
[04:00:24 -119649.637117] SLOW spr round 8 (radius: 10)
[04:02:32 -119647.199492] SLOW spr round 9 (radius: 5)
[04:04:36 -119647.199488] SLOW spr round 10 (radius: 10)
[04:06:33 -119647.199487] SLOW spr round 11 (radius: 15)
[04:08:57 -119647.199485] SLOW spr round 12 (radius: 20)
[04:12:07 -119647.199484] SLOW spr round 13 (radius: 25)
[04:15:58 -119646.219524] SLOW spr round 14 (radius: 5)
[04:18:14 -119643.803830] SLOW spr round 15 (radius: 5)
[04:20:15 -119643.803635] SLOW spr round 16 (radius: 10)
[04:22:11 -119643.803634] SLOW spr round 17 (radius: 15)
[04:24:37 -119643.803633] SLOW spr round 18 (radius: 20)
[04:27:47 -119643.803632] SLOW spr round 19 (radius: 25)
[04:31:38 -119643.803630] Model parameter optimization (eps = 0.100000)

[04:31:44] ML tree search #4, logLikelihood: -119643.768488

[04:31:44 -570042.469139] Initial branch length optimization
[04:31:46 -431545.708447] Model parameter optimization (eps = 10.000000)
[04:32:18 -430111.417035] AUTODETECT spr round 1 (radius: 5)
[04:34:06 -289676.023106] AUTODETECT spr round 2 (radius: 10)
[04:36:04 -196787.107805] AUTODETECT spr round 3 (radius: 15)
[04:38:06 -173131.810853] AUTODETECT spr round 4 (radius: 20)
[04:40:28 -154771.795066] AUTODETECT spr round 5 (radius: 25)
[04:43:26 -142223.960663] SPR radius for FAST iterations: 25 (autodetect)
[04:43:26 -142223.960663] Model parameter optimization (eps = 3.000000)
[04:43:47 -142017.527054] FAST spr round 1 (radius: 25)
[04:45:56 -120915.436945] FAST spr round 2 (radius: 25)
[04:47:49 -119783.231038] FAST spr round 3 (radius: 25)
[04:49:32 -119743.066456] FAST spr round 4 (radius: 25)
[04:51:09 -119724.173781] FAST spr round 5 (radius: 25)
[04:52:41 -119724.172358] Model parameter optimization (eps = 1.000000)
[04:52:56 -119719.240518] SLOW spr round 1 (radius: 5)
[04:54:44 -119700.570089] SLOW spr round 2 (radius: 5)
[04:56:31 -119689.880733] SLOW spr round 3 (radius: 5)
[04:58:19 -119684.145141] SLOW spr round 4 (radius: 5)
[05:00:02 -119684.144409] SLOW spr round 5 (radius: 10)
[05:01:52 -119680.925344] SLOW spr round 6 (radius: 5)
[05:04:02 -119680.877761] SLOW spr round 7 (radius: 10)
[05:06:02 -119678.159849] SLOW spr round 8 (radius: 5)
[05:08:06 -119678.159493] SLOW spr round 9 (radius: 10)
[05:10:04 -119678.159469] SLOW spr round 10 (radius: 15)
[05:12:30 -119653.092052] SLOW spr round 11 (radius: 5)
[05:14:45 -119635.469268] SLOW spr round 12 (radius: 5)
[05:16:45 -119625.669623] SLOW spr round 13 (radius: 5)
[05:18:38 -119623.422261] SLOW spr round 14 (radius: 5)
[05:20:29 -119620.638985] SLOW spr round 15 (radius: 5)
[05:22:18 -119620.636211] SLOW spr round 16 (radius: 10)
[05:24:09 -119620.635793] SLOW spr round 17 (radius: 15)
[05:26:41 -119620.635710] SLOW spr round 18 (radius: 20)
[05:29:49 -119620.635693] SLOW spr round 19 (radius: 25)
[05:33:52 -119620.635690] Model parameter optimization (eps = 0.100000)

[05:34:02] ML tree search #5, logLikelihood: -119620.417232

[05:34:02 -572085.410785] Initial branch length optimization
[05:34:04 -432455.414671] Model parameter optimization (eps = 10.000000)
[05:34:28 -431024.124017] AUTODETECT spr round 1 (radius: 5)
[05:36:14 -284762.024181] AUTODETECT spr round 2 (radius: 10)
[05:38:08 -213636.942175] AUTODETECT spr round 3 (radius: 15)
[05:40:08 -184338.549268] AUTODETECT spr round 4 (radius: 20)
[05:42:29 -167144.710636] AUTODETECT spr round 5 (radius: 25)
[05:45:25 -151624.768618] SPR radius for FAST iterations: 25 (autodetect)
[05:45:25 -151624.768618] Model parameter optimization (eps = 3.000000)
[05:45:51 -151392.072060] FAST spr round 1 (radius: 25)
[05:48:22 -122271.895284] FAST spr round 2 (radius: 25)
[05:50:20 -120078.820063] FAST spr round 3 (radius: 25)
[05:52:06 -119693.357378] FAST spr round 4 (radius: 25)
[05:53:47 -119667.060777] FAST spr round 5 (radius: 25)
[05:55:22 -119665.324952] FAST spr round 6 (radius: 25)
[05:56:57 -119664.888972] FAST spr round 7 (radius: 25)
[05:58:29 -119664.888203] Model parameter optimization (eps = 1.000000)
[05:58:47 -119646.868010] SLOW spr round 1 (radius: 5)
[06:00:39 -119628.925570] SLOW spr round 2 (radius: 5)
[06:02:30 -119627.302166] SLOW spr round 3 (radius: 5)
[06:04:18 -119627.301727] SLOW spr round 4 (radius: 10)
[06:06:10 -119625.895844] SLOW spr round 5 (radius: 5)
[06:08:18 -119625.851478] SLOW spr round 6 (radius: 10)
[06:10:19 -119625.851310] SLOW spr round 7 (radius: 15)
[06:12:49 -119624.504386] SLOW spr round 8 (radius: 5)
[06:15:00 -119624.504299] SLOW spr round 9 (radius: 10)
[06:17:04 -119624.504247] SLOW spr round 10 (radius: 15)
[06:19:29 -119624.504195] SLOW spr round 11 (radius: 20)
[06:22:38 -119624.503746] SLOW spr round 12 (radius: 25)
[06:26:31 -119624.503693] Model parameter optimization (eps = 0.100000)

[06:26:36] ML tree search #6, logLikelihood: -119624.439612

[06:26:37 -570820.776808] Initial branch length optimization
[06:26:39 -431266.336475] Model parameter optimization (eps = 10.000000)
[06:27:04 -429944.851771] AUTODETECT spr round 1 (radius: 5)
[06:28:52 -281799.284593] AUTODETECT spr round 2 (radius: 10)
[06:30:46 -213601.801093] AUTODETECT spr round 3 (radius: 15)
[06:32:54 -159731.771320] AUTODETECT spr round 4 (radius: 20)
[06:35:11 -139631.482436] AUTODETECT spr round 5 (radius: 25)
[06:37:40 -137017.501401] SPR radius for FAST iterations: 25 (autodetect)
[06:37:40 -137017.501401] Model parameter optimization (eps = 3.000000)
[06:38:05 -136840.589496] FAST spr round 1 (radius: 25)
[06:40:13 -120369.564514] FAST spr round 2 (radius: 25)
[06:42:02 -119789.035329] FAST spr round 3 (radius: 25)
[06:43:42 -119703.561436] FAST spr round 4 (radius: 25)
[06:45:19 -119684.014052] FAST spr round 5 (radius: 25)
[06:46:51 -119680.347627] FAST spr round 6 (radius: 25)
[06:48:20 -119676.986027] FAST spr round 7 (radius: 25)
[06:49:48 -119676.985750] Model parameter optimization (eps = 1.000000)
[06:50:01 -119675.434268] SLOW spr round 1 (radius: 5)
[06:51:46 -119645.154520] SLOW spr round 2 (radius: 5)
[06:53:32 -119637.197847] SLOW spr round 3 (radius: 5)
[06:55:20 -119631.668246] SLOW spr round 4 (radius: 5)
[06:57:06 -119631.668152] SLOW spr round 5 (radius: 10)
[06:58:57 -119629.193474] SLOW spr round 6 (radius: 5)
[07:01:04 -119629.166247] SLOW spr round 7 (radius: 10)
[07:03:03 -119629.166127] SLOW spr round 8 (radius: 15)
[07:05:30 -119629.166106] SLOW spr round 9 (radius: 20)
[07:08:46 -119629.165712] SLOW spr round 10 (radius: 25)
[07:12:35 -119626.636049] SLOW spr round 11 (radius: 5)
[07:14:37 -119626.636030] SLOW spr round 12 (radius: 10)
[07:16:34 -119626.636027] SLOW spr round 13 (radius: 15)
[07:18:48 -119626.636027] SLOW spr round 14 (radius: 20)
[07:21:48 -119625.142799] SLOW spr round 15 (radius: 5)
[07:23:48 -119625.142736] SLOW spr round 16 (radius: 10)
[07:25:43 -119625.142736] SLOW spr round 17 (radius: 15)
[07:27:58 -119625.142736] SLOW spr round 18 (radius: 20)
[07:31:01 -119625.142736] SLOW spr round 19 (radius: 25)
[07:34:54 -119625.142736] Model parameter optimization (eps = 0.100000)

[07:35:02] ML tree search #7, logLikelihood: -119625.028231

[07:35:02 -570166.765813] Initial branch length optimization
[07:35:04 -433521.178269] Model parameter optimization (eps = 10.000000)
[07:35:32 -432093.771106] AUTODETECT spr round 1 (radius: 5)
[07:37:12 -287104.640421] AUTODETECT spr round 2 (radius: 10)
[07:38:55 -217884.016617] AUTODETECT spr round 3 (radius: 15)
[07:40:44 -187514.997074] AUTODETECT spr round 4 (radius: 20)
[07:42:44 -164843.005856] AUTODETECT spr round 5 (radius: 25)
[07:45:02 -143869.769740] SPR radius for FAST iterations: 25 (autodetect)
[07:45:02 -143869.769740] Model parameter optimization (eps = 3.000000)
[07:45:24 -143653.977455] FAST spr round 1 (radius: 25)
[07:47:22 -121292.680697] FAST spr round 2 (radius: 25)
[07:49:02 -119826.936115] FAST spr round 3 (radius: 25)
[07:50:33 -119734.778598] FAST spr round 4 (radius: 25)
[07:52:01 -119724.631067] FAST spr round 5 (radius: 25)
[07:53:26 -119724.630264] Model parameter optimization (eps = 1.000000)
[07:53:43 -119721.631966] SLOW spr round 1 (radius: 5)
[07:55:24 -119691.001896] SLOW spr round 2 (radius: 5)
[07:57:04 -119685.942079] SLOW spr round 3 (radius: 5)
[07:58:41 -119685.941690] SLOW spr round 4 (radius: 10)
[08:00:21 -119681.245191] SLOW spr round 5 (radius: 5)
[08:02:15 -119681.217766] SLOW spr round 6 (radius: 10)
[08:04:04 -119679.040193] SLOW spr round 7 (radius: 5)
[08:05:56 -119679.039977] SLOW spr round 8 (radius: 10)
[08:07:41 -119679.039977] SLOW spr round 9 (radius: 15)
[08:09:54 -119679.039976] SLOW spr round 10 (radius: 20)
[08:12:48 -119677.661314] SLOW spr round 11 (radius: 5)
[08:14:47 -119677.661313] SLOW spr round 12 (radius: 10)
[08:16:42 -119677.661312] SLOW spr round 13 (radius: 15)
[08:18:52 -119677.661312] SLOW spr round 14 (radius: 20)
[08:21:47 -119677.661312] SLOW spr round 15 (radius: 25)
[08:25:25 -119669.694061] SLOW spr round 16 (radius: 5)
[08:27:25 -119668.880299] SLOW spr round 17 (radius: 5)
[08:29:12 -119668.879873] SLOW spr round 18 (radius: 10)
[08:30:53 -119668.879870] SLOW spr round 19 (radius: 15)
[08:33:01 -119668.879870] SLOW spr round 20 (radius: 20)
[08:35:25 -119668.879870] SLOW spr round 21 (radius: 25)
[08:38:31 -119668.879870] Model parameter optimization (eps = 0.100000)

[08:38:36] ML tree search #8, logLikelihood: -119668.861319

[08:38:36 -572890.281446] Initial branch length optimization
[08:38:38 -428993.373096] Model parameter optimization (eps = 10.000000)
[08:38:57 -427597.890913] AUTODETECT spr round 1 (radius: 5)
[08:40:18 -284424.518825] AUTODETECT spr round 2 (radius: 10)
[08:41:46 -208174.368888] AUTODETECT spr round 3 (radius: 15)
[08:43:20 -167976.683311] AUTODETECT spr round 4 (radius: 20)
[08:45:05 -145163.379963] AUTODETECT spr round 5 (radius: 25)
[08:46:54 -140854.773920] SPR radius for FAST iterations: 25 (autodetect)
[08:46:54 -140854.773920] Model parameter optimization (eps = 3.000000)
[08:47:11 -140685.045145] FAST spr round 1 (radius: 25)
[08:48:56 -120914.053339] FAST spr round 2 (radius: 25)
[08:50:24 -119748.156029] FAST spr round 3 (radius: 25)
[08:51:41 -119658.189079] FAST spr round 4 (radius: 25)
[08:52:54 -119654.825390] FAST spr round 5 (radius: 25)
[08:54:03 -119654.813271] Model parameter optimization (eps = 1.000000)
[08:54:15 -119642.172996] SLOW spr round 1 (radius: 5)
[08:55:39 -119632.258554] SLOW spr round 2 (radius: 5)
[08:57:01 -119631.774362] SLOW spr round 3 (radius: 5)
[08:58:21 -119631.773547] SLOW spr round 4 (radius: 10)
[08:59:44 -119629.137514] SLOW spr round 5 (radius: 5)
[09:01:19 -119629.137130] SLOW spr round 6 (radius: 10)
[09:02:49 -119629.137113] SLOW spr round 7 (radius: 15)
[09:04:39 -119628.879039] SLOW spr round 8 (radius: 5)
[09:06:18 -119628.873232] SLOW spr round 9 (radius: 10)
[09:07:52 -119628.873232] SLOW spr round 10 (radius: 15)
[09:09:42 -119628.873232] SLOW spr round 11 (radius: 20)
[09:12:08 -119627.541314] SLOW spr round 12 (radius: 5)
[09:13:48 -119627.541314] SLOW spr round 13 (radius: 10)
[09:15:24 -119627.541314] SLOW spr round 14 (radius: 15)
[09:17:14 -119627.541314] SLOW spr round 15 (radius: 20)
[09:19:39 -119627.541314] SLOW spr round 16 (radius: 25)
[09:22:47 -119626.569748] SLOW spr round 17 (radius: 5)
[09:24:29 -119626.443470] SLOW spr round 18 (radius: 5)
[09:26:01 -119626.441463] SLOW spr round 19 (radius: 10)
[09:27:27 -119626.441375] SLOW spr round 20 (radius: 15)
[09:29:20 -119626.441375] SLOW spr round 21 (radius: 20)
[09:31:44 -119626.441375] SLOW spr round 22 (radius: 25)
[09:34:52 -119626.441375] Model parameter optimization (eps = 0.100000)

[09:34:58] ML tree search #9, logLikelihood: -119626.316622

[09:34:58 -576829.678541] Initial branch length optimization
[09:35:00 -434499.251762] Model parameter optimization (eps = 10.000000)
[09:35:25 -433056.732171] AUTODETECT spr round 1 (radius: 5)
[09:36:47 -282753.896552] AUTODETECT spr round 2 (radius: 10)
[09:38:12 -213833.990919] AUTODETECT spr round 3 (radius: 15)
[09:39:46 -185976.550789] AUTODETECT spr round 4 (radius: 20)
[09:41:37 -144251.919601] AUTODETECT spr round 5 (radius: 25)
[09:43:36 -138150.158314] SPR radius for FAST iterations: 25 (autodetect)
[09:43:36 -138150.158314] Model parameter optimization (eps = 3.000000)
[09:43:52 -137977.912769] FAST spr round 1 (radius: 25)
[09:45:34 -120742.743114] FAST spr round 2 (radius: 25)
[09:47:00 -119750.734178] FAST spr round 3 (radius: 25)
[09:48:17 -119686.121625] FAST spr round 4 (radius: 25)
[09:49:29 -119679.304842] FAST spr round 5 (radius: 25)
[09:50:39 -119679.303034] Model parameter optimization (eps = 1.000000)
[09:50:49 -119674.668765] SLOW spr round 1 (radius: 5)
[09:52:11 -119654.441360] SLOW spr round 2 (radius: 5)
[09:53:33 -119641.890136] SLOW spr round 3 (radius: 5)
[09:54:55 -119636.487071] SLOW spr round 4 (radius: 5)
[09:56:17 -119636.485774] SLOW spr round 5 (radius: 10)
[09:57:40 -119632.852766] SLOW spr round 6 (radius: 5)
[09:59:19 -119631.143718] SLOW spr round 7 (radius: 5)
[10:00:47 -119631.143243] SLOW spr round 8 (radius: 10)
[10:02:12 -119631.143205] SLOW spr round 9 (radius: 15)
[10:04:08 -119631.142594] SLOW spr round 10 (radius: 20)
[10:06:40 -119629.830533] SLOW spr round 11 (radius: 5)
[10:08:21 -119629.830240] SLOW spr round 12 (radius: 10)
[10:09:57 -119629.830210] SLOW spr round 13 (radius: 15)
[10:11:48 -119629.830182] SLOW spr round 14 (radius: 20)
[10:14:30 -119629.830154] SLOW spr round 15 (radius: 25)
[10:18:22 -119629.830127] Model parameter optimization (eps = 0.100000)

[10:18:31] ML tree search #10, logLikelihood: -119629.633012

[10:18:31 -566994.407317] Initial branch length optimization
[10:18:33 -430046.852484] Model parameter optimization (eps = 10.000000)
[10:18:55 -428550.876591] AUTODETECT spr round 1 (radius: 5)
[10:20:26 -287592.901195] AUTODETECT spr round 2 (radius: 10)
[10:22:03 -212424.307750] AUTODETECT spr round 3 (radius: 15)
[10:23:46 -171504.849784] AUTODETECT spr round 4 (radius: 20)
[10:25:42 -149034.086328] AUTODETECT spr round 5 (radius: 25)
[10:27:51 -142935.549666] SPR radius for FAST iterations: 25 (autodetect)
[10:27:51 -142935.549666] Model parameter optimization (eps = 3.000000)
[10:28:09 -142719.518582] FAST spr round 1 (radius: 25)
[10:30:07 -121235.298344] FAST spr round 2 (radius: 25)
[10:31:44 -119761.567375] FAST spr round 3 (radius: 25)
[10:33:14 -119693.864812] FAST spr round 4 (radius: 25)
[10:34:35 -119687.771243] FAST spr round 5 (radius: 25)
[10:35:53 -119687.770981] Model parameter optimization (eps = 1.000000)
[10:36:05 -119681.286622] SLOW spr round 1 (radius: 5)
[10:37:40 -119639.225288] SLOW spr round 2 (radius: 5)
[10:39:13 -119630.498909] SLOW spr round 3 (radius: 5)
[10:40:40 -119630.498772] SLOW spr round 4 (radius: 10)
[10:42:13 -119626.129325] SLOW spr round 5 (radius: 5)
[10:43:59 -119626.129042] SLOW spr round 6 (radius: 10)
[10:45:39 -119626.129028] SLOW spr round 7 (radius: 15)
[10:47:42 -119626.128554] SLOW spr round 8 (radius: 20)
[10:50:17 -119624.790522] SLOW spr round 9 (radius: 5)
[10:52:08 -119624.790521] SLOW spr round 10 (radius: 10)
[10:53:55 -119624.790521] SLOW spr round 11 (radius: 15)
[10:55:57 -119624.790323] SLOW spr round 12 (radius: 20)
[10:58:34 -119624.790323] SLOW spr round 13 (radius: 25)
[11:01:52 -119623.820173] SLOW spr round 14 (radius: 5)
[11:03:54 -119623.692795] SLOW spr round 15 (radius: 5)
[11:05:44 -119623.690931] SLOW spr round 16 (radius: 10)
[11:07:28 -119623.690871] SLOW spr round 17 (radius: 15)
[11:09:39 -119623.690871] SLOW spr round 18 (radius: 20)
[11:12:21 -119623.690871] SLOW spr round 19 (radius: 25)
[11:15:44 -119623.690871] Model parameter optimization (eps = 0.100000)

[11:15:51] ML tree search #11, logLikelihood: -119623.633781

[11:15:51 -566069.669796] Initial branch length optimization
[11:15:53 -432827.980943] Model parameter optimization (eps = 10.000000)
[11:16:24 -431097.379702] AUTODETECT spr round 1 (radius: 5)
[11:17:58 -283326.035845] AUTODETECT spr round 2 (radius: 10)
[11:19:39 -208172.390708] AUTODETECT spr round 3 (radius: 15)
[11:21:28 -170325.889813] AUTODETECT spr round 4 (radius: 20)
[11:23:23 -145370.871182] AUTODETECT spr round 5 (radius: 25)
[11:25:33 -138571.958412] SPR radius for FAST iterations: 25 (autodetect)
[11:25:33 -138571.958412] Model parameter optimization (eps = 3.000000)
[11:25:53 -138372.253526] FAST spr round 1 (radius: 25)
[11:27:51 -120880.864077] FAST spr round 2 (radius: 25)
[11:29:24 -119731.539536] FAST spr round 3 (radius: 25)
[11:30:48 -119664.360417] FAST spr round 4 (radius: 25)
[11:32:07 -119648.410593] FAST spr round 5 (radius: 25)
[11:33:23 -119646.047446] FAST spr round 6 (radius: 25)
[11:34:38 -119646.046738] Model parameter optimization (eps = 1.000000)
[11:34:50 -119644.920227] SLOW spr round 1 (radius: 5)
[11:36:19 -119628.683620] SLOW spr round 2 (radius: 5)
[11:37:46 -119628.680762] SLOW spr round 3 (radius: 10)
[11:39:16 -119627.303208] SLOW spr round 4 (radius: 5)
[11:41:00 -119625.052278] SLOW spr round 5 (radius: 5)
[11:42:36 -119625.052119] SLOW spr round 6 (radius: 10)
[11:44:14 -119625.052117] SLOW spr round 7 (radius: 15)
[11:46:26 -119623.488312] SLOW spr round 8 (radius: 5)
[11:48:21 -119622.317976] SLOW spr round 9 (radius: 5)
[11:50:02 -119622.317891] SLOW spr round 10 (radius: 10)
[11:51:35 -119622.317851] SLOW spr round 11 (radius: 15)
[11:53:37 -119622.317850] SLOW spr round 12 (radius: 20)
[11:56:20 -119620.930857] SLOW spr round 13 (radius: 5)
[11:58:08 -119620.930814] SLOW spr round 14 (radius: 10)
[11:59:52 -119620.930774] SLOW spr round 15 (radius: 15)
[12:01:49 -119620.930351] SLOW spr round 16 (radius: 20)
[12:04:33 -119620.929886] SLOW spr round 17 (radius: 25)
[12:08:06 -119619.516880] SLOW spr round 18 (radius: 5)
[12:09:57 -119619.516590] SLOW spr round 19 (radius: 10)
[12:11:42 -119619.516588] SLOW spr round 20 (radius: 15)
[12:13:39 -119619.516588] SLOW spr round 21 (radius: 20)
[12:16:24 -119619.516587] SLOW spr round 22 (radius: 25)
[12:19:57 -119619.516587] Model parameter optimization (eps = 0.100000)

[12:20:01] ML tree search #12, logLikelihood: -119619.503266

[12:20:01 -569594.629568] Initial branch length optimization
[12:20:03 -430765.300230] Model parameter optimization (eps = 10.000000)
[12:20:26 -429290.179397] AUTODETECT spr round 1 (radius: 5)
[12:21:56 -282128.206652] AUTODETECT spr round 2 (radius: 10)
[12:23:32 -210856.803866] AUTODETECT spr round 3 (radius: 15)
[12:25:11 -172860.240077] AUTODETECT spr round 4 (radius: 20)
[12:26:55 -154759.446170] AUTODETECT spr round 5 (radius: 25)
[12:28:58 -143686.021123] SPR radius for FAST iterations: 25 (autodetect)
[12:28:58 -143686.021123] Model parameter optimization (eps = 3.000000)
[12:29:21 -143521.014109] FAST spr round 1 (radius: 25)
[12:31:11 -120671.631900] FAST spr round 2 (radius: 25)
[12:32:43 -119742.995677] FAST spr round 3 (radius: 25)
[12:34:08 -119686.231194] FAST spr round 4 (radius: 25)
[12:35:29 -119674.655846] FAST spr round 5 (radius: 25)
[12:36:47 -119671.141572] FAST spr round 6 (radius: 25)
[12:38:04 -119671.139770] Model parameter optimization (eps = 1.000000)
[12:38:18 -119666.091781] SLOW spr round 1 (radius: 5)
[12:39:50 -119633.002597] SLOW spr round 2 (radius: 5)
[12:41:21 -119622.239561] SLOW spr round 3 (radius: 5)
[12:42:51 -119611.574714] SLOW spr round 4 (radius: 5)
[12:44:22 -119611.392659] SLOW spr round 5 (radius: 5)
[12:45:51 -119610.332830] SLOW spr round 6 (radius: 5)
[12:47:20 -119610.332325] SLOW spr round 7 (radius: 10)
[12:48:52 -119608.686812] SLOW spr round 8 (radius: 5)
[12:50:42 -119604.860111] SLOW spr round 9 (radius: 5)
[12:52:24 -119604.859740] SLOW spr round 10 (radius: 10)
[12:54:02 -119604.859651] SLOW spr round 11 (radius: 15)
[12:56:14 -119604.859195] SLOW spr round 12 (radius: 20)
[12:59:01 -119603.510881] SLOW spr round 13 (radius: 5)
[13:01:01 -119603.510813] SLOW spr round 14 (radius: 10)
[13:02:53 -119603.510756] SLOW spr round 15 (radius: 15)
[13:04:59 -119603.510697] SLOW spr round 16 (radius: 20)
[13:07:50 -119603.510638] SLOW spr round 17 (radius: 25)
[13:11:29 -119603.510578] Model parameter optimization (eps = 0.100000)

[13:11:39] ML tree search #13, logLikelihood: -119602.964267

[13:11:39 -568335.015218] Initial branch length optimization
[13:11:42 -426766.206248] Model parameter optimization (eps = 10.000000)
[13:12:08 -425348.531147] AUTODETECT spr round 1 (radius: 5)
[13:13:42 -280122.645303] AUTODETECT spr round 2 (radius: 10)
[13:15:22 -208837.152979] AUTODETECT spr round 3 (radius: 15)
[13:17:09 -176680.028933] AUTODETECT spr round 4 (radius: 20)
[13:19:13 -150877.804300] AUTODETECT spr round 5 (radius: 25)
[13:21:21 -142068.449887] SPR radius for FAST iterations: 25 (autodetect)
[13:21:21 -142068.449887] Model parameter optimization (eps = 3.000000)
[13:21:36 -141898.908908] FAST spr round 1 (radius: 25)
[13:23:29 -121100.957946] FAST spr round 2 (radius: 25)
[13:25:03 -119786.556521] FAST spr round 3 (radius: 25)
[13:26:26 -119665.642779] FAST spr round 4 (radius: 25)
[13:27:44 -119658.865352] FAST spr round 5 (radius: 25)
[13:28:59 -119658.864092] Model parameter optimization (eps = 1.000000)
[13:29:08 -119656.980920] SLOW spr round 1 (radius: 5)
[13:30:39 -119637.406645] SLOW spr round 2 (radius: 5)
[13:32:07 -119634.853006] SLOW spr round 3 (radius: 5)
[13:33:33 -119634.852393] SLOW spr round 4 (radius: 10)
[13:35:02 -119631.882378] SLOW spr round 5 (radius: 5)
[13:36:45 -119631.855126] SLOW spr round 6 (radius: 10)
[13:38:22 -119631.854929] SLOW spr round 7 (radius: 15)
[13:40:20 -119631.854268] SLOW spr round 8 (radius: 20)
[13:42:59 -119631.854215] SLOW spr round 9 (radius: 25)
[13:46:21 -119631.854163] Model parameter optimization (eps = 0.100000)

[13:46:26] ML tree search #14, logLikelihood: -119631.795572

[13:46:26 -568476.361607] Initial branch length optimization
[13:46:28 -431642.069486] Model parameter optimization (eps = 10.000000)
[13:46:53 -430169.967359] AUTODETECT spr round 1 (radius: 5)
[13:48:23 -288002.310604] AUTODETECT spr round 2 (radius: 10)
[13:50:03 -210915.358605] AUTODETECT spr round 3 (radius: 15)
[13:51:44 -180901.156147] AUTODETECT spr round 4 (radius: 20)
[13:53:38 -159490.291123] AUTODETECT spr round 5 (radius: 25)
[13:55:38 -151224.400386] SPR radius for FAST iterations: 25 (autodetect)
[13:55:38 -151224.400386] Model parameter optimization (eps = 3.000000)
[13:56:08 -151007.678427] FAST spr round 1 (radius: 25)
[13:58:07 -124268.327699] FAST spr round 2 (radius: 25)
[13:59:45 -119995.519392] FAST spr round 3 (radius: 25)
[14:01:15 -119747.269638] FAST spr round 4 (radius: 25)
[14:02:41 -119677.013357] FAST spr round 5 (radius: 25)
[14:04:02 -119677.011994] Model parameter optimization (eps = 1.000000)
[14:04:16 -119658.700875] SLOW spr round 1 (radius: 5)
[14:05:54 -119644.293061] SLOW spr round 2 (radius: 5)
[14:07:31 -119641.150478] SLOW spr round 3 (radius: 5)
[14:09:06 -119641.149919] SLOW spr round 4 (radius: 10)
[14:10:44 -119640.231582] SLOW spr round 5 (radius: 5)
[14:12:39 -119634.057233] SLOW spr round 6 (radius: 5)
[14:14:21 -119634.056903] SLOW spr round 7 (radius: 10)
[14:16:02 -119632.853545] SLOW spr round 8 (radius: 5)
[14:17:54 -119632.054888] SLOW spr round 9 (radius: 5)
[14:19:35 -119632.054524] SLOW spr round 10 (radius: 10)
[14:21:15 -119632.054173] SLOW spr round 11 (radius: 15)
[14:23:31 -119632.053825] SLOW spr round 12 (radius: 20)
[14:26:30 -119630.724896] SLOW spr round 13 (radius: 5)
[14:28:27 -119630.724549] SLOW spr round 14 (radius: 10)
[14:30:20 -119630.724211] SLOW spr round 15 (radius: 15)
[14:32:31 -119630.723877] SLOW spr round 16 (radius: 20)
[14:35:31 -119630.723545] SLOW spr round 17 (radius: 25)
[14:39:23 -119630.723216] Model parameter optimization (eps = 0.100000)

[14:39:32] ML tree search #15, logLikelihood: -119630.538708

[14:39:32 -568871.607121] Initial branch length optimization
[14:39:34 -431711.089325] Model parameter optimization (eps = 10.000000)
[14:39:58 -430201.038124] AUTODETECT spr round 1 (radius: 5)
[14:41:34 -290120.828537] AUTODETECT spr round 2 (radius: 10)
[14:43:15 -207136.217860] AUTODETECT spr round 3 (radius: 15)
[14:45:04 -167518.095729] AUTODETECT spr round 4 (radius: 20)
[14:47:09 -148518.146714] AUTODETECT spr round 5 (radius: 25)
[14:49:40 -137305.756760] SPR radius for FAST iterations: 25 (autodetect)
[14:49:40 -137305.756760] Model parameter optimization (eps = 3.000000)
[14:50:00 -137146.367839] FAST spr round 1 (radius: 25)
[14:51:57 -120470.189372] FAST spr round 2 (radius: 25)
[14:53:33 -119788.967572] FAST spr round 3 (radius: 25)
[14:55:02 -119675.338382] FAST spr round 4 (radius: 25)
[14:56:27 -119657.169441] FAST spr round 5 (radius: 25)
[14:57:49 -119657.123719] Model parameter optimization (eps = 1.000000)
[14:57:59 -119654.110811] SLOW spr round 1 (radius: 5)
[14:59:37 -119627.828095] SLOW spr round 2 (radius: 5)
[15:01:14 -119623.404525] SLOW spr round 3 (radius: 5)
[15:02:51 -119620.391407] SLOW spr round 4 (radius: 5)
[15:04:26 -119620.390919] SLOW spr round 5 (radius: 10)
[15:06:03 -119619.083872] SLOW spr round 6 (radius: 5)
[15:07:58 -119618.010323] SLOW spr round 7 (radius: 5)
[15:09:41 -119617.646075] SLOW spr round 8 (radius: 5)
[15:11:19 -119617.645915] SLOW spr round 9 (radius: 10)
[15:12:56 -119617.645815] SLOW spr round 10 (radius: 15)
[15:15:11 -119617.645778] SLOW spr round 11 (radius: 20)
[15:18:02 -119613.461879] SLOW spr round 12 (radius: 5)
[15:19:52 -119613.461559] SLOW spr round 13 (radius: 10)
[15:21:36 -119613.461423] SLOW spr round 14 (radius: 15)
[15:23:35 -119613.460978] SLOW spr round 15 (radius: 20)
[15:26:19 -119613.460977] SLOW spr round 16 (radius: 25)
[15:29:52 -119613.460976] Model parameter optimization (eps = 0.100000)

[15:29:58] ML tree search #16, logLikelihood: -119613.298238

[15:29:58 -565028.925691] Initial branch length optimization
[15:30:00 -429158.236444] Model parameter optimization (eps = 10.000000)
[15:30:27 -427749.495758] AUTODETECT spr round 1 (radius: 5)
[15:31:55 -286660.352452] AUTODETECT spr round 2 (radius: 10)
[15:33:30 -207205.176904] AUTODETECT spr round 3 (radius: 15)
[15:35:15 -173374.514155] AUTODETECT spr round 4 (radius: 20)
[15:37:04 -164979.889097] AUTODETECT spr round 5 (radius: 25)
[15:39:09 -155072.545735] SPR radius for FAST iterations: 25 (autodetect)
[15:39:09 -155072.545735] Model parameter optimization (eps = 3.000000)
[15:39:26 -154845.302927] FAST spr round 1 (radius: 25)
[15:41:22 -124983.062865] FAST spr round 2 (radius: 25)
[15:42:56 -120295.107859] FAST spr round 3 (radius: 25)
[15:44:21 -119762.781886] FAST spr round 4 (radius: 25)
[15:45:41 -119653.703162] FAST spr round 5 (radius: 25)
[15:47:00 -119653.581222] FAST spr round 6 (radius: 25)
[15:48:16 -119653.580558] Model parameter optimization (eps = 1.000000)
[15:48:30 -119643.804524] SLOW spr round 1 (radius: 5)
[15:50:00 -119629.383711] SLOW spr round 2 (radius: 5)
[15:51:27 -119629.382608] SLOW spr round 3 (radius: 10)
[15:52:59 -119628.487501] SLOW spr round 4 (radius: 5)
[15:54:44 -119628.460532] SLOW spr round 5 (radius: 10)
[15:56:25 -119628.460396] SLOW spr round 6 (radius: 15)
[15:58:28 -119626.003976] SLOW spr round 7 (radius: 5)
[16:00:16 -119626.003956] SLOW spr round 8 (radius: 10)
[16:02:00 -119626.003945] SLOW spr round 9 (radius: 15)
[16:04:02 -119626.003933] SLOW spr round 10 (radius: 20)
[16:06:43 -119626.003922] SLOW spr round 11 (radius: 25)
[16:10:02 -119625.036027] SLOW spr round 12 (radius: 5)
[16:11:54 -119624.904175] SLOW spr round 13 (radius: 5)
[16:13:34 -119624.903476] SLOW spr round 14 (radius: 10)
[16:15:10 -119624.903455] SLOW spr round 15 (radius: 15)
[16:17:14 -119624.903440] SLOW spr round 16 (radius: 20)
[16:19:55 -119624.903424] SLOW spr round 17 (radius: 25)
[16:23:16 -119624.903409] Model parameter optimization (eps = 0.100000)

[16:23:21] ML tree search #17, logLikelihood: -119624.872079

[16:23:21 -571459.267662] Initial branch length optimization
[16:23:23 -431630.578491] Model parameter optimization (eps = 10.000000)
[16:23:46 -430249.945808] AUTODETECT spr round 1 (radius: 5)
[16:25:15 -279767.654863] AUTODETECT spr round 2 (radius: 10)
[16:26:50 -204521.388126] AUTODETECT spr round 3 (radius: 15)
[16:28:27 -169080.561166] AUTODETECT spr round 4 (radius: 20)
[16:30:14 -155823.802871] AUTODETECT spr round 5 (radius: 25)
[16:32:14 -144050.117146] SPR radius for FAST iterations: 25 (autodetect)
[16:32:14 -144050.117146] Model parameter optimization (eps = 3.000000)
[16:32:35 -143839.374698] FAST spr round 1 (radius: 25)
[16:34:31 -121819.358300] FAST spr round 2 (radius: 25)
[16:36:06 -119843.228716] FAST spr round 3 (radius: 25)
[16:37:36 -119673.659224] FAST spr round 4 (radius: 25)
[16:38:58 -119662.614943] FAST spr round 5 (radius: 25)
[16:40:14 -119659.895702] FAST spr round 6 (radius: 25)
[16:41:31 -119659.883970] Model parameter optimization (eps = 1.000000)
[16:41:44 -119650.031750] SLOW spr round 1 (radius: 5)
[16:43:17 -119620.877039] SLOW spr round 2 (radius: 5)
[16:44:47 -119618.162246] SLOW spr round 3 (radius: 5)
[16:46:17 -119618.161767] SLOW spr round 4 (radius: 10)
[16:47:49 -119616.873590] SLOW spr round 5 (radius: 5)
[16:49:42 -119616.847784] SLOW spr round 6 (radius: 10)
[16:51:28 -119616.847592] SLOW spr round 7 (radius: 15)
[16:53:37 -119616.846939] SLOW spr round 8 (radius: 20)
[16:56:27 -119615.502321] SLOW spr round 9 (radius: 5)
[16:58:22 -119615.501438] SLOW spr round 10 (radius: 10)
[17:00:08 -119615.500866] SLOW spr round 11 (radius: 15)
[17:02:07 -119615.500800] SLOW spr round 12 (radius: 20)
[17:04:44 -119615.500732] SLOW spr round 13 (radius: 25)
[17:08:05 -119614.026235] SLOW spr round 14 (radius: 5)
[17:09:59 -119614.026082] SLOW spr round 15 (radius: 10)
[17:11:50 -119614.025952] SLOW spr round 16 (radius: 15)
[17:13:52 -119614.025879] SLOW spr round 17 (radius: 20)
[17:16:41 -119612.520880] SLOW spr round 18 (radius: 5)
[17:18:34 -119612.520752] SLOW spr round 19 (radius: 10)
[17:20:19 -119612.520675] SLOW spr round 20 (radius: 15)
[17:22:17 -119612.520597] SLOW spr round 21 (radius: 20)
[17:24:59 -119612.520518] SLOW spr round 22 (radius: 25)
[17:28:24 -119611.558793] SLOW spr round 23 (radius: 5)
[17:30:15 -119611.431587] SLOW spr round 24 (radius: 5)
[17:31:53 -119611.429206] SLOW spr round 25 (radius: 10)
[17:33:27 -119611.428897] SLOW spr round 26 (radius: 15)
[17:35:28 -119611.428895] SLOW spr round 27 (radius: 20)
[17:38:01 -119611.428895] SLOW spr round 28 (radius: 25)
[17:41:21 -119610.571389] SLOW spr round 29 (radius: 5)
[17:43:12 -119607.724173] SLOW spr round 30 (radius: 5)
[17:44:52 -119607.253236] SLOW spr round 31 (radius: 5)
[17:46:24 -119607.253007] SLOW spr round 32 (radius: 10)
[17:47:54 -119607.253001] SLOW spr round 33 (radius: 15)
[17:49:56 -119607.253000] SLOW spr round 34 (radius: 20)
[17:52:27 -119607.253000] SLOW spr round 35 (radius: 25)
[17:55:48 -119607.252999] Model parameter optimization (eps = 0.100000)

[17:55:53] ML tree search #18, logLikelihood: -119607.145442

[17:55:53 -564404.965728] Initial branch length optimization
[17:55:56 -430821.919541] Model parameter optimization (eps = 10.000000)
[17:56:20 -429294.513916] AUTODETECT spr round 1 (radius: 5)
[17:57:48 -289229.368471] AUTODETECT spr round 2 (radius: 10)
[17:59:24 -212358.259338] AUTODETECT spr round 3 (radius: 15)
[18:01:02 -189389.206862] AUTODETECT spr round 4 (radius: 20)
[18:02:57 -160782.501841] AUTODETECT spr round 5 (radius: 25)
[18:05:06 -148174.044234] SPR radius for FAST iterations: 25 (autodetect)
[18:05:06 -148174.044234] Model parameter optimization (eps = 3.000000)
[18:05:20 -148023.358481] FAST spr round 1 (radius: 25)
[18:07:07 -121487.762124] FAST spr round 2 (radius: 25)
[18:08:34 -119791.735408] FAST spr round 3 (radius: 25)
[18:09:55 -119717.136904] FAST spr round 4 (radius: 25)
[18:11:12 -119700.245892] FAST spr round 5 (radius: 25)
[18:12:27 -119700.245722] Model parameter optimization (eps = 1.000000)
[18:12:39 -119693.671875] SLOW spr round 1 (radius: 5)
[18:14:07 -119661.790856] SLOW spr round 2 (radius: 5)
[18:15:35 -119659.023812] SLOW spr round 3 (radius: 5)
[18:16:59 -119659.023744] SLOW spr round 4 (radius: 10)
[18:18:28 -119652.359603] SLOW spr round 5 (radius: 5)
[18:20:10 -119650.529655] SLOW spr round 6 (radius: 5)
[18:21:41 -119650.529620] SLOW spr round 7 (radius: 10)
[18:23:11 -119650.529617] SLOW spr round 8 (radius: 15)
[18:25:09 -119650.529034] SLOW spr round 9 (radius: 20)
[18:27:41 -119649.121621] SLOW spr round 10 (radius: 5)
[18:29:28 -119649.121506] SLOW spr round 11 (radius: 10)
[18:31:09 -119649.121506] SLOW spr round 12 (radius: 15)
[18:32:57 -119649.121506] SLOW spr round 13 (radius: 20)
[18:35:22 -119649.121505] SLOW spr round 14 (radius: 25)
[18:38:31 -119632.082955] SLOW spr round 15 (radius: 5)
[18:40:12 -119629.411974] SLOW spr round 16 (radius: 5)
[18:41:43 -119629.411957] SLOW spr round 17 (radius: 10)
[18:43:10 -119629.411957] SLOW spr round 18 (radius: 15)
[18:45:00 -119629.411957] SLOW spr round 19 (radius: 20)
[18:47:25 -119629.411956] SLOW spr round 20 (radius: 25)
[18:50:33 -119629.411956] Model parameter optimization (eps = 0.100000)

[18:50:39] ML tree search #19, logLikelihood: -119629.288357

[18:50:39 -566853.628693] Initial branch length optimization
[18:50:41 -428072.614456] Model parameter optimization (eps = 10.000000)
[18:51:06 -426709.406224] AUTODETECT spr round 1 (radius: 5)
[18:52:26 -277962.290336] AUTODETECT spr round 2 (radius: 10)
[18:54:10 -201761.018251] AUTODETECT spr round 3 (radius: 15)
[18:56:05 -164948.736920] AUTODETECT spr round 4 (radius: 20)
[18:58:21 -152870.759838] AUTODETECT spr round 5 (radius: 25)
[19:00:35 -143087.060499] SPR radius for FAST iterations: 25 (autodetect)
[19:00:35 -143087.060499] Model parameter optimization (eps = 3.000000)
[19:00:52 -142948.923361] FAST spr round 1 (radius: 25)
[19:03:04 -126804.519663] FAST spr round 2 (radius: 25)
[19:05:00 -121324.702203] FAST spr round 3 (radius: 25)
[19:06:41 -119688.782155] FAST spr round 4 (radius: 25)
[19:08:18 -119647.774847] FAST spr round 5 (radius: 25)
[19:09:45 -119647.763279] Model parameter optimization (eps = 1.000000)
[19:09:59 -119644.637081] SLOW spr round 1 (radius: 5)
[19:11:48 -119624.845389] SLOW spr round 2 (radius: 5)
[19:13:32 -119615.021979] SLOW spr round 3 (radius: 5)
[19:15:15 -119612.438774] SLOW spr round 4 (radius: 5)
[19:16:54 -119612.438366] SLOW spr round 5 (radius: 10)
[19:18:38 -119612.173543] SLOW spr round 6 (radius: 5)
[19:20:41 -119610.732538] SLOW spr round 7 (radius: 5)
[19:22:33 -119608.829632] SLOW spr round 8 (radius: 5)
[19:24:17 -119608.829615] SLOW spr round 9 (radius: 10)
[19:26:02 -119608.829610] SLOW spr round 10 (radius: 15)
[19:28:29 -119608.829022] SLOW spr round 11 (radius: 20)
[19:31:35 -119607.534476] SLOW spr round 12 (radius: 5)
[19:33:42 -119607.534470] SLOW spr round 13 (radius: 10)
[19:35:53 -119607.534465] SLOW spr round 14 (radius: 15)
[19:38:12 -119607.534459] SLOW spr round 15 (radius: 20)
[19:41:19 -119607.534454] SLOW spr round 16 (radius: 25)
[19:45:14 -119605.567920] SLOW spr round 17 (radius: 5)
[19:47:21 -119605.543557] SLOW spr round 18 (radius: 10)
[19:49:23 -119605.541158] SLOW spr round 19 (radius: 15)
[19:51:43 -119605.538742] SLOW spr round 20 (radius: 20)
[19:54:51 -119605.537884] SLOW spr round 21 (radius: 25)
[19:58:44 -119605.537869] Model parameter optimization (eps = 0.100000)

[19:58:50] ML tree search #20, logLikelihood: -119605.409896


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.179722,0.304430) (0.136660,0.286910) (0.361171,0.735603) (0.322446,1.986064) 
   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: -119599.894216

AIC score: 243209.788432 / AICc score: 8287269.788432 / BIC score: 251639.926746
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=495).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQM7/3_mltree/Q9UQM7.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQM7/3_mltree/Q9UQM7.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQM7/3_mltree/Q9UQM7.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQM7/3_mltree/Q9UQM7.raxml.log

Analysis started: 05-Jul-2021 00:12:38 / finished: 05-Jul-2021 20:11:30

Elapsed time: 71931.239 seconds

Consumed energy: 5944.433 Wh (= 30 km in an electric car, or 149 km with an e-scooter!)