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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 30-Jun-2021 17:09:07 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P48058/2_msa/P48058_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P48058/3_mltree/P48058 --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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P48058/2_msa/P48058_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 742 sites

WARNING: Sequences tr_A0A1D5PFB0_A0A1D5PFB0_CHICK_9031 and tr_R0LJL7_R0LJL7_ANAPL_8839 are exactly identical!
WARNING: Sequences sp_P23819_GRIA2_MOUSE_10090 and sp_P19491_GRIA2_RAT_10116 are exactly identical!
WARNING: Sequences sp_Q9Z2W8_GRIA4_MOUSE_10090 and tr_M3Y4L9_M3Y4L9_MUSPF_9669 are exactly identical!
WARNING: Sequences sp_Q9Z2W8_GRIA4_MOUSE_10090 and tr_A0A287CSZ6_A0A287CSZ6_ICTTR_43179 are exactly identical!
WARNING: Sequences sp_Q9Z2W8_GRIA4_MOUSE_10090 and tr_A0A091DS90_A0A091DS90_FUKDA_885580 are exactly identical!
WARNING: Sequences tr_M3Y321_M3Y321_MUSPF_9669 and tr_G1R3B7_G1R3B7_NOMLE_61853 are exactly identical!
WARNING: Sequences tr_M3Y321_M3Y321_MUSPF_9669 and tr_A0A287CX18_A0A287CX18_ICTTR_43179 are exactly identical!
WARNING: Sequences tr_M3Y321_M3Y321_MUSPF_9669 and tr_A0A286XH79_A0A286XH79_CAVPO_10141 are exactly identical!
WARNING: Sequences tr_M3Y321_M3Y321_MUSPF_9669 and sp_P42262_GRIA2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_M3Y321_M3Y321_MUSPF_9669 and tr_F7HC11_F7HC11_CALJA_9483 are exactly identical!
WARNING: Sequences tr_M3Y321_M3Y321_MUSPF_9669 and tr_A0A287AEG6_A0A287AEG6_PIG_9823 are exactly identical!
WARNING: Sequences tr_M3Y321_M3Y321_MUSPF_9669 and tr_F1MBY1_F1MBY1_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_M3Y321_M3Y321_MUSPF_9669 and tr_A0A2I2UTP4_A0A2I2UTP4_FELCA_9685 are exactly identical!
WARNING: Sequences tr_M3Y321_M3Y321_MUSPF_9669 and tr_A0A096MWL5_A0A096MWL5_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_M3Y321_M3Y321_MUSPF_9669 and tr_A0A2K6AX90_A0A2K6AX90_MACNE_9545 are exactly identical!
WARNING: Sequences tr_M3YTJ1_M3YTJ1_MUSPF_9669 and tr_F1PWT6_F1PWT6_CANLF_9615 are exactly identical!
WARNING: Sequences tr_M3YTJ1_M3YTJ1_MUSPF_9669 and tr_A0A287ATF5_A0A287ATF5_PIG_9823 are exactly identical!
WARNING: Sequences tr_M3YTJ1_M3YTJ1_MUSPF_9669 and tr_F1MCM2_F1MCM2_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_M3YTJ1_M3YTJ1_MUSPF_9669 and tr_A0A2Y9EKB9_A0A2Y9EKB9_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_M3YTJ1_M3YTJ1_MUSPF_9669 and tr_A0A384CDU9_A0A384CDU9_URSMA_29073 are exactly identical!
WARNING: Sequences tr_Q9VDH5_Q9VDH5_DROME_7227 and tr_B4II60_B4II60_DROSE_7238 are exactly identical!
WARNING: Sequences tr_A0A2I3GH36_A0A2I3GH36_NOMLE_61853 and tr_A0A2I2Z6L3_A0A2I2Z6L3_GORGO_9595 are exactly identical!
WARNING: Sequences tr_A0A2I3GH36_A0A2I3GH36_NOMLE_61853 and tr_G1SKJ0_G1SKJ0_RABIT_9986 are exactly identical!
WARNING: Sequences tr_A0A2I3GH36_A0A2I3GH36_NOMLE_61853 and tr_C7G3L5_C7G3L5_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I3GH36_A0A2I3GH36_NOMLE_61853 and tr_I3MFS2_I3MFS2_ICTTR_43179 are exactly identical!
WARNING: Sequences tr_A0A2I3GH36_A0A2I3GH36_NOMLE_61853 and sp_Q13002_GRIK2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3GH36_A0A2I3GH36_NOMLE_61853 and tr_H9EM65_H9EM65_MACMU_9544 are exactly identical!
WARNING: Sequences tr_A0A2I3GH36_A0A2I3GH36_NOMLE_61853 and tr_F7IBF1_F7IBF1_CALJA_9483 are exactly identical!
WARNING: Sequences tr_A0A2I3GH36_A0A2I3GH36_NOMLE_61853 and tr_A0A2I3NA05_A0A2I3NA05_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I3GH36_A0A2I3GH36_NOMLE_61853 and tr_A0A2K5LJ69_A0A2K5LJ69_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3GH36_A0A2I3GH36_NOMLE_61853 and tr_A0A2K6BKA4_A0A2K6BKA4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3GH36_A0A2I3GH36_NOMLE_61853 and tr_A0A2R9BEK2_A0A2R9BEK2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3GMM7_A0A2I3GMM7_NOMLE_61853 and tr_G1U6F6_G1U6F6_RABIT_9986 are exactly identical!
WARNING: Sequences tr_A0A2I3GMM7_A0A2I3GMM7_NOMLE_61853 and tr_A0A2I3TR48_A0A2I3TR48_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I3GMM7_A0A2I3GMM7_NOMLE_61853 and tr_F7D1C2_F7D1C2_CALJA_9483 are exactly identical!
WARNING: Sequences tr_A0A2I3GMM7_A0A2I3GMM7_NOMLE_61853 and tr_A0A286ZS63_A0A286ZS63_PIG_9823 are exactly identical!
WARNING: Sequences tr_A0A2I3GMM7_A0A2I3GMM7_NOMLE_61853 and tr_A0A2Y9IJY5_A0A2Y9IJY5_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A2I3H5V1_A0A2I3H5V1_NOMLE_61853 and tr_G3R2A6_G3R2A6_GORGO_9595 are exactly identical!
WARNING: Sequences tr_A0A2I3H5V1_A0A2I3H5V1_NOMLE_61853 and tr_A0A2J8WWH6_A0A2J8WWH6_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I3H5V1_A0A2I3H5V1_NOMLE_61853 and tr_A0A2J8LE31_A0A2J8LE31_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I3H5V1_A0A2I3H5V1_NOMLE_61853 and sp_P42263_GRIA3_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3H5V1_A0A2I3H5V1_NOMLE_61853 and tr_A0A096N5U4_A0A096N5U4_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I3H5V1_A0A2I3H5V1_NOMLE_61853 and tr_A0A2K6C368_A0A2K6C368_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3H5V1_A0A2I3H5V1_NOMLE_61853 and tr_A0A2K5XAG2_A0A2K5XAG2_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G1R6G6_G1R6G6_NOMLE_61853 and tr_G3RLF8_G3RLF8_GORGO_9595 are exactly identical!
WARNING: Sequences tr_G1R6G6_G1R6G6_NOMLE_61853 and tr_A0A2J8XXC2_A0A2J8XXC2_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G1R6G6_G1R6G6_NOMLE_61853 and sp_P48058_GRIA4_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1R6G6_G1R6G6_NOMLE_61853 and tr_A0A2R8P4U6_A0A2R8P4U6_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G1R6G6_G1R6G6_NOMLE_61853 and tr_G7PNL9_G7PNL9_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G1R6G6_G1R6G6_NOMLE_61853 and tr_A0A096MR99_A0A096MR99_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G1R6G6_G1R6G6_NOMLE_61853 and tr_A0A2K5N3Y1_A0A2K5N3Y1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1R6G6_G1R6G6_NOMLE_61853 and tr_A0A2K5YF63_A0A2K5YF63_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G1R6G6_G1R6G6_NOMLE_61853 and tr_A0A2R8ZUD5_A0A2R8ZUD5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G1PBG8_G1PBG8_MYOLU_59463 and tr_F1P7K6_F1P7K6_CANLF_9615 are exactly identical!
WARNING: Sequences tr_G1PBG8_G1PBG8_MYOLU_59463 and tr_F6VNJ0_F6VNJ0_HORSE_9796 are exactly identical!
WARNING: Sequences tr_G1PBG8_G1PBG8_MYOLU_59463 and tr_F1MG21_F1MG21_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_G1PBG8_G1PBG8_MYOLU_59463 and tr_A0A337S2R5_A0A337S2R5_FELCA_9685 are exactly identical!
WARNING: Sequences tr_G1PBG8_G1PBG8_MYOLU_59463 and tr_A0A2Y9L356_A0A2Y9L356_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G1PBG8_G1PBG8_MYOLU_59463 and tr_A0A384D8V4_A0A384D8V4_URSMA_29073 are exactly identical!
WARNING: Sequences tr_A0A2I2YZC6_A0A2I2YZC6_GORGO_9595 and tr_A0A2I3T979_A0A2I3T979_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2YZC6_A0A2I2YZC6_GORGO_9595 and tr_F7AGW3_F7AGW3_MACMU_9544 are exactly identical!
WARNING: Sequences tr_A0A2I2YZC6_A0A2I2YZC6_GORGO_9595 and tr_A0A2I3MXB9_A0A2I3MXB9_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I2YZC6_A0A2I2YZC6_GORGO_9595 and tr_A0A2K5M9E6_A0A2K5M9E6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I2YZC6_A0A2I2YZC6_GORGO_9595 and tr_A0A2K5YKW4_A0A2K5YKW4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I2ZAY3_A0A2I2ZAY3_GORGO_9595 and tr_F1PDP9_F1PDP9_CANLF_9615 are exactly identical!
WARNING: Sequences tr_A0A2I2ZAY3_A0A2I2ZAY3_GORGO_9595 and tr_F6XW64_F6XW64_HORSE_9796 are exactly identical!
WARNING: Sequences tr_A0A2I2ZAY3_A0A2I2ZAY3_GORGO_9595 and sp_P42261_GRIA1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2ZAY3_A0A2I2ZAY3_GORGO_9595 and tr_A0A1D5RJF9_A0A1D5RJF9_MACMU_9544 are exactly identical!
WARNING: Sequences tr_A0A2I2ZAY3_A0A2I2ZAY3_GORGO_9595 and tr_G1M786_G1M786_AILME_9646 are exactly identical!
WARNING: Sequences tr_A0A2I2ZAY3_A0A2I2ZAY3_GORGO_9595 and tr_G7P8R7_G7P8R7_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A2I2ZAY3_A0A2I2ZAY3_GORGO_9595 and tr_A0A2I2USC9_A0A2I2USC9_FELCA_9685 are exactly identical!
WARNING: Sequences tr_A0A2I2ZAY3_A0A2I2ZAY3_GORGO_9595 and tr_A0A2K5N2C7_A0A2K5N2C7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I2ZAY3_A0A2I2ZAY3_GORGO_9595 and tr_A0A2K5ZIF1_A0A2K5ZIF1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I2ZAY3_A0A2I2ZAY3_GORGO_9595 and tr_A0A2R9A4P9_A0A2R9A4P9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I2ZAY3_A0A2I2ZAY3_GORGO_9595 and tr_A0A2Y9DB28_A0A2Y9DB28_TRIMA_127582 are exactly identical!
WARNING: Sequences tr_A0A2I2ZAY3_A0A2I2ZAY3_GORGO_9595 and tr_A0A384C725_A0A384C725_URSMA_29073 are exactly identical!
WARNING: Sequences tr_G3RAA1_G3RAA1_GORGO_9595 and tr_H2PEL6_H2PEL6_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3RAA1_G3RAA1_GORGO_9595 and tr_G1TGQ2_G1TGQ2_RABIT_9986 are exactly identical!
WARNING: Sequences tr_G3RAA1_G3RAA1_GORGO_9595 and tr_H2QQC5_H2QQC5_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RAA1_G3RAA1_GORGO_9595 and tr_F6QNJ8_F6QNJ8_HORSE_9796 are exactly identical!
WARNING: Sequences tr_G3RAA1_G3RAA1_GORGO_9595 and tr_W5P8A7_W5P8A7_SHEEP_9940 are exactly identical!
WARNING: Sequences tr_G3RAA1_G3RAA1_GORGO_9595 and tr_A0A2K5M0L7_A0A2K5M0L7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G3RAA1_G3RAA1_GORGO_9595 and tr_A0A2K5ZBU0_A0A2K5ZBU0_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G3RAA1_G3RAA1_GORGO_9595 and tr_A0A2R9BL79_A0A2R9BL79_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G1SD16_G1SD16_RABIT_9986 and tr_W5PVI2_W5PVI2_SHEEP_9940 are exactly identical!
WARNING: Sequences tr_G1SD16_G1SD16_RABIT_9986 and tr_A0A2U4CHR8_A0A2U4CHR8_TURTR_9739 are exactly identical!
WARNING: Sequences tr_G1SD16_G1SD16_RABIT_9986 and tr_A0A2Y9MEW1_A0A2Y9MEW1_DELLE_9749 are exactly identical!
WARNING: Sequences tr_G1SD16_G1SD16_RABIT_9986 and tr_A0A2Y9SYW0_A0A2Y9SYW0_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_G1TP65_G1TP65_RABIT_9986 and tr_A0A1U7TYV5_A0A1U7TYV5_TARSY_1868482 are exactly identical!
WARNING: Sequences tr_E2RHU1_E2RHU1_CANLF_9615 and tr_F6Q8I9_F6Q8I9_HORSE_9796 are exactly identical!
WARNING: Sequences tr_F1PHA8_F1PHA8_CANLF_9615 and tr_A0A2Y9K6Q2_A0A2Y9K6Q2_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A2I3T3T7_A0A2I3T3T7_PANTR_9598 and tr_F7AGS3_F7AGS3_MACMU_9544 are exactly identical!
WARNING: Sequences tr_A0A2I3T3T7_A0A2I3T3T7_PANTR_9598 and tr_A0A0D9S295_A0A0D9S295_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I3T3T7_A0A2I3T3T7_PANTR_9598 and tr_A0A2K6DC70_A0A2K6DC70_MACNE_9545 are exactly identical!
WARNING: Sequences sp_Q5IS46_GRIK4_PANTR_9598 and sp_Q16099_GRIK4_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_W5PPF9_W5PPF9_SHEEP_9940 and tr_G1LFW5_G1LFW5_AILME_9646 are exactly identical!
WARNING: Sequences tr_M4A267_M4A267_XIPMA_8083 and tr_A0A087X543_A0A087X543_POEFO_48698 are exactly identical!
WARNING: Sequences tr_G3T7Y3_G3T7Y3_LOXAF_9785 and tr_G1M8E3_G1M8E3_AILME_9646 are exactly identical!
WARNING: Sequences tr_G3T7Y3_G3T7Y3_LOXAF_9785 and tr_A0A2I2U7P0_A0A2I2U7P0_FELCA_9685 are exactly identical!
WARNING: Sequences tr_G3T7Y3_G3T7Y3_LOXAF_9785 and tr_A0A2U3VXH1_A0A2U3VXH1_ODORO_9708 are exactly identical!
WARNING: Sequences tr_H0ZR22_H0ZR22_TAEGU_59729 and tr_A0A091EIB5_A0A091EIB5_CORBR_85066 are exactly identical!
WARNING: Sequences tr_H0ZR22_H0ZR22_TAEGU_59729 and tr_A0A093SB17_A0A093SB17_9PASS_328815 are exactly identical!
WARNING: Sequences tr_F7I9V3_F7I9V3_CALJA_9483 and tr_A0A2Y9KMA4_A0A2Y9KMA4_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_F1RYR0_F1RYR0_PIG_9823 and tr_L5JKX4_L5JKX4_PTEAL_9402 are exactly identical!
WARNING: Sequences tr_G1L0S8_G1L0S8_AILME_9646 and tr_A0A2U3WTU7_A0A2U3WTU7_ODORO_9708 are exactly identical!
WARNING: Sequences tr_G1L0S8_G1L0S8_AILME_9646 and tr_A0A2Y9K518_A0A2Y9K518_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G1L0S8_G1L0S8_AILME_9646 and tr_A0A384C0F1_A0A384C0F1_URSMA_29073 are exactly identical!
WARNING: Sequences tr_G1M6N9_G1M6N9_AILME_9646 and tr_A0A3Q0DCJ1_A0A3Q0DCJ1_TARSY_1868482 are exactly identical!
WARNING: Sequences tr_G7Q3M1_G7Q3M1_MACFA_9541 and tr_A0A2K5MNX8_A0A2K5MNX8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7Q3M1_G7Q3M1_MACFA_9541 and tr_A0A2R8ZQ00_A0A2R8ZQ00_PANPA_9597 are exactly identical!
WARNING: Sequences tr_U3JRV6_U3JRV6_FICAL_59894 and tr_A0A091F134_A0A091F134_CORBR_85066 are exactly identical!
WARNING: Sequences tr_U3JRV6_U3JRV6_FICAL_59894 and tr_A0A091ISM6_A0A091ISM6_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_U3JRV6_U3JRV6_FICAL_59894 and tr_A0A091W1F9_A0A091W1F9_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_U3JRV6_U3JRV6_FICAL_59894 and tr_A0A091G917_A0A091G917_9AVES_55661 are exactly identical!
WARNING: Sequences tr_U3JRV6_U3JRV6_FICAL_59894 and tr_A0A0A0B3D5_A0A0A0B3D5_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_U3JRV6_U3JRV6_FICAL_59894 and tr_A0A2I0MVA5_A0A2I0MVA5_COLLI_8932 are exactly identical!
WARNING: Sequences tr_U3JRV6_U3JRV6_FICAL_59894 and tr_A0A093GEY1_A0A093GEY1_DRYPU_118200 are exactly identical!
WARNING: Sequences tr_U3JRV6_U3JRV6_FICAL_59894 and tr_A0A218ULZ1_A0A218ULZ1_9PASE_299123 are exactly identical!
WARNING: Sequences tr_R0K213_R0K213_ANAPL_8839 and tr_A0A091JHV7_A0A091JHV7_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_R0K213_R0K213_ANAPL_8839 and tr_A0A093HKG3_A0A093HKG3_STRCA_441894 are exactly identical!
WARNING: Sequences tr_R0K213_R0K213_ANAPL_8839 and tr_A0A091WFF2_A0A091WFF2_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_R0K213_R0K213_ANAPL_8839 and tr_A0A091GQD3_A0A091GQD3_9AVES_55661 are exactly identical!
WARNING: Sequences tr_R0K213_R0K213_ANAPL_8839 and tr_A0A0A0AVN2_A0A0A0AVN2_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_U3I8K4_U3I8K4_ANAPL_8839 and tr_A0A091JCX4_A0A091JCX4_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_U3I8K4_U3I8K4_ANAPL_8839 and tr_A0A091VVX4_A0A091VVX4_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_U3I8K4_U3I8K4_ANAPL_8839 and tr_A0A091W2N8_A0A091W2N8_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A2I3MW59_A0A2I3MW59_PAPAN_9555 and tr_A0A0D9S7R9_A0A0D9S7R9_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I3MW59_A0A2I3MW59_PAPAN_9555 and tr_A0A2K5N1M9_A0A2K5N1M9_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3MW59_A0A2I3MW59_PAPAN_9555 and tr_A0A2K6CHA5_A0A2K6CHA5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I3MW59_A0A2I3MW59_PAPAN_9555 and tr_A0A2K5YEJ2_A0A2K5YEJ2_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A091DHR5_A0A091DHR5_FUKDA_885580 and tr_A0A0D9RQB5_A0A0D9RQB5_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A151NQC1_A0A151NQC1_ALLMI_8496 and tr_A0A1U7RWT3_A0A1U7RWT3_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A091EXD8_A0A091EXD8_CORBR_85066 and tr_A0A218UDF0_A0A218UDF0_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A0A091F5C4_A0A091F5C4_CORBR_85066 and tr_A0A093HL69_A0A093HL69_STRCA_441894 are exactly identical!
WARNING: Sequences tr_A0A091INJ8_A0A091INJ8_EGRGA_188379 and tr_A0A091V702_A0A091V702_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091INJ8_A0A091INJ8_EGRGA_188379 and tr_A0A087REV3_A0A087REV3_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091INJ8_A0A091INJ8_EGRGA_188379 and tr_A0A0A0B1W8_A0A0A0B1W8_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A091J2D2_A0A091J2D2_EGRGA_188379 and tr_A0A091VMF1_A0A091VMF1_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091J2D2_A0A091J2D2_EGRGA_188379 and tr_A0A087QUE3_A0A087QUE3_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091JB59_A0A091JB59_EGRGA_188379 and tr_A0A091VM91_A0A091VM91_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091JB59_A0A091JB59_EGRGA_188379 and tr_A0A087RCM9_A0A087RCM9_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091JB59_A0A091JB59_EGRGA_188379 and tr_A0A0A0A7T4_A0A0A0A7T4_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A091USH9_A0A091USH9_NIPNI_128390 and tr_A0A091IFW5_A0A091IFW5_CALAN_9244 are exactly identical!
WARNING: Sequences tr_A0A087R9W2_A0A087R9W2_APTFO_9233 and tr_A0A0A0B332_A0A0A0B332_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A2I0MCQ1_A0A2I0MCQ1_COLLI_8932 and tr_A0A1V4J902_A0A1V4J902_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A0V1NX75_A0A0V1NX75_9BILA_92180 and tr_A0A0V0TSM8_A0A0V0TSM8_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A1U7QL28_A0A1U7QL28_MESAU_10036 and tr_A0A2U3VHX9_A0A2U3VHX9_ODORO_9708 are exactly identical!
WARNING: Sequences tr_A0A1U7QL28_A0A1U7QL28_MESAU_10036 and tr_A0A2U3XNC4_A0A2U3XNC4_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_A0A1U7QL28_A0A1U7QL28_MESAU_10036 and tr_A0A2Y9KH47_A0A2Y9KH47_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A1U7QL28_A0A1U7QL28_MESAU_10036 and tr_A0A384BNB1_A0A384BNB1_URSMA_29073 are exactly identical!
WARNING: Sequences tr_A0A226NFU6_A0A226NFU6_CALSU_9009 and tr_A0A226PEN6_A0A226PEN6_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0T1Z9_A0A2D0T1Z9_ICTPU_7998 and tr_A0A2D0T2W7_A0A2D0T2W7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U4ANA3_A0A2U4ANA3_TURTR_9739 and tr_A0A2Y9P6V8_A0A2Y9P6V8_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2Y9LHC8_A0A2Y9LHC8_DELLE_9749 and tr_A0A2Y9SCV8_A0A2Y9SCV8_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2Y9LHC8_A0A2Y9LHC8_DELLE_9749 and tr_A0A383Z3N2_A0A383Z3N2_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 155

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P48058/3_mltree/P48058.raxml.reduced.phy

Alignment comprises 1 partitions and 742 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 742 / 742
Gaps: 4.07 %
Invariant sites: 0.94 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P48058/3_mltree/P48058.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 / 106 / 8480
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1045851.954929] Initial branch length optimization
[00:00:04 -834349.082877] Model parameter optimization (eps = 10.000000)
[00:00:43 -833562.854596] AUTODETECT spr round 1 (radius: 5)
[00:02:54 -485733.343840] AUTODETECT spr round 2 (radius: 10)
[00:05:15 -325520.508292] AUTODETECT spr round 3 (radius: 15)
[00:07:39 -246727.649431] AUTODETECT spr round 4 (radius: 20)
[00:10:12 -228283.941298] AUTODETECT spr round 5 (radius: 25)
[00:13:10 -209003.913876] SPR radius for FAST iterations: 25 (autodetect)
[00:13:10 -209003.913876] Model parameter optimization (eps = 3.000000)
[00:13:37 -208706.296716] FAST spr round 1 (radius: 25)
[00:16:04 -165079.833394] FAST spr round 2 (radius: 25)
[00:18:05 -159204.482708] FAST spr round 3 (radius: 25)
[00:19:55 -158820.388500] FAST spr round 4 (radius: 25)
[00:21:33 -158794.054367] FAST spr round 5 (radius: 25)
[00:23:05 -158793.292713] FAST spr round 6 (radius: 25)
[00:24:37 -158789.674803] FAST spr round 7 (radius: 25)
[00:26:07 -158789.674130] Model parameter optimization (eps = 1.000000)
[00:26:21 -158786.649503] SLOW spr round 1 (radius: 5)
[00:28:13 -158752.716051] SLOW spr round 2 (radius: 5)
[00:30:04 -158751.493733] SLOW spr round 3 (radius: 5)
[00:31:57 -158751.493369] SLOW spr round 4 (radius: 10)
[00:33:53 -158751.447727] SLOW spr round 5 (radius: 15)
[00:36:42 -158751.447694] SLOW spr round 6 (radius: 20)
[00:41:10 -158751.447667] SLOW spr round 7 (radius: 25)
[00:47:42 -158751.447641] Model parameter optimization (eps = 0.100000)

[00:47:47] ML tree search #1, logLikelihood: -158751.414980

[00:47:47 -1053707.169428] Initial branch length optimization
[00:47:50 -832634.097918] Model parameter optimization (eps = 10.000000)
[00:48:20 -831935.628468] AUTODETECT spr round 1 (radius: 5)
[00:50:31 -477527.270723] AUTODETECT spr round 2 (radius: 10)
[00:52:50 -313551.134831] AUTODETECT spr round 3 (radius: 15)
[00:55:14 -251205.018605] AUTODETECT spr round 4 (radius: 20)
[00:57:45 -228650.296400] AUTODETECT spr round 5 (radius: 25)
[01:00:37 -212655.896378] SPR radius for FAST iterations: 25 (autodetect)
[01:00:37 -212655.896378] Model parameter optimization (eps = 3.000000)
[01:01:02 -212268.624495] FAST spr round 1 (radius: 25)
[01:03:21 -165529.724625] FAST spr round 2 (radius: 25)
[01:05:14 -159450.245161] FAST spr round 3 (radius: 25)
[01:06:54 -158866.015683] FAST spr round 4 (radius: 25)
[01:08:33 -158844.559934] FAST spr round 5 (radius: 25)
[01:10:05 -158844.559053] Model parameter optimization (eps = 1.000000)
[01:10:16 -158842.668803] SLOW spr round 1 (radius: 5)
[01:12:09 -158813.866066] SLOW spr round 2 (radius: 5)
[01:14:03 -158812.484120] SLOW spr round 3 (radius: 5)
[01:15:55 -158812.483771] SLOW spr round 4 (radius: 10)
[01:17:52 -158812.483024] SLOW spr round 5 (radius: 15)
[01:20:41 -158812.483004] SLOW spr round 6 (radius: 20)
[01:24:56 -158811.946855] SLOW spr round 7 (radius: 5)
[01:27:19 -158811.946801] SLOW spr round 8 (radius: 10)
[01:29:35 -158811.946774] SLOW spr round 9 (radius: 15)
[01:32:14 -158811.946760] SLOW spr round 10 (radius: 20)
[01:36:40 -158811.946747] SLOW spr round 11 (radius: 25)
[01:42:25 -158808.360624] SLOW spr round 12 (radius: 5)
[01:44:54 -158779.440716] SLOW spr round 13 (radius: 5)
[01:47:04 -158775.568274] SLOW spr round 14 (radius: 5)
[01:49:02 -158775.568247] SLOW spr round 15 (radius: 10)
[01:50:59 -158775.568232] SLOW spr round 16 (radius: 15)
[01:53:50 -158775.568217] SLOW spr round 17 (radius: 20)
[01:58:21 -158775.568202] SLOW spr round 18 (radius: 25)
[02:04:21 -158775.568188] Model parameter optimization (eps = 0.100000)

[02:04:26] ML tree search #2, logLikelihood: -158775.549593

[02:04:26 -1053570.425363] Initial branch length optimization
[02:04:31 -843674.745529] Model parameter optimization (eps = 10.000000)
[02:04:57 -843020.509571] AUTODETECT spr round 1 (radius: 5)
[02:07:08 -485557.222608] AUTODETECT spr round 2 (radius: 10)
[02:09:30 -324767.107717] AUTODETECT spr round 3 (radius: 15)
[02:11:53 -256626.451086] AUTODETECT spr round 4 (radius: 20)
[02:14:32 -244073.624100] AUTODETECT spr round 5 (radius: 25)
[02:17:33 -207817.514001] SPR radius for FAST iterations: 25 (autodetect)
[02:17:33 -207817.514001] Model parameter optimization (eps = 3.000000)
[02:17:56 -207531.489523] FAST spr round 1 (radius: 25)
[02:20:16 -172963.038370] FAST spr round 2 (radius: 25)
[02:22:13 -164521.446911] FAST spr round 3 (radius: 25)
[02:23:59 -159103.922461] FAST spr round 4 (radius: 25)
[02:25:39 -158837.625135] FAST spr round 5 (radius: 25)
[02:27:14 -158830.605972] FAST spr round 6 (radius: 25)
[02:28:47 -158830.605926] Model parameter optimization (eps = 1.000000)
[02:29:04 -158816.255687] SLOW spr round 1 (radius: 5)
[02:30:58 -158777.427055] SLOW spr round 2 (radius: 5)
[02:32:54 -158773.341724] SLOW spr round 3 (radius: 5)
[02:34:51 -158771.545253] SLOW spr round 4 (radius: 5)
[02:36:44 -158770.623383] SLOW spr round 5 (radius: 5)
[02:38:36 -158770.623302] SLOW spr round 6 (radius: 10)
[02:40:36 -158768.170276] SLOW spr round 7 (radius: 5)
[02:42:50 -158768.170207] SLOW spr round 8 (radius: 10)
[02:44:57 -158768.170196] SLOW spr round 9 (radius: 15)
[02:47:38 -158768.170186] SLOW spr round 10 (radius: 20)
[02:52:15 -158768.170175] SLOW spr round 11 (radius: 25)
[02:58:34 -158768.170165] Model parameter optimization (eps = 0.100000)

[02:58:45] ML tree search #3, logLikelihood: -158768.062386

[02:58:45 -1058640.606350] Initial branch length optimization
[02:58:49 -839954.767230] Model parameter optimization (eps = 10.000000)
[02:59:21 -839286.835545] AUTODETECT spr round 1 (radius: 5)
[03:01:33 -491092.342927] AUTODETECT spr round 2 (radius: 10)
[03:03:51 -343303.546738] AUTODETECT spr round 3 (radius: 15)
[03:06:13 -265016.194062] AUTODETECT spr round 4 (radius: 20)
[03:09:05 -205581.049205] AUTODETECT spr round 5 (radius: 25)
[03:12:00 -194791.960296] SPR radius for FAST iterations: 25 (autodetect)
[03:12:00 -194791.960296] Model parameter optimization (eps = 3.000000)
[03:12:24 -194458.540675] FAST spr round 1 (radius: 25)
[03:14:39 -160383.128494] FAST spr round 2 (radius: 25)
[03:16:24 -159035.630867] FAST spr round 3 (radius: 25)
[03:18:04 -158898.044369] FAST spr round 4 (radius: 25)
[03:19:38 -158890.516551] FAST spr round 5 (radius: 25)
[03:21:09 -158888.129286] FAST spr round 6 (radius: 25)
[03:22:38 -158888.129263] Model parameter optimization (eps = 1.000000)
[03:22:50 -158884.918247] SLOW spr round 1 (radius: 5)
[03:24:41 -158856.152916] SLOW spr round 2 (radius: 5)
[03:26:33 -158835.297749] SLOW spr round 3 (radius: 5)
[03:28:25 -158835.297421] SLOW spr round 4 (radius: 10)
[03:30:18 -158835.275795] SLOW spr round 5 (radius: 15)
[03:33:10 -158825.964692] SLOW spr round 6 (radius: 5)
[03:35:30 -158802.723136] SLOW spr round 7 (radius: 5)
[03:37:34 -158802.723081] SLOW spr round 8 (radius: 10)
[03:39:31 -158802.723062] SLOW spr round 9 (radius: 15)
[03:42:18 -158794.072919] SLOW spr round 10 (radius: 5)
[03:44:36 -158794.072800] SLOW spr round 11 (radius: 10)
[03:46:46 -158794.072781] SLOW spr round 12 (radius: 15)
[03:49:27 -158794.072765] SLOW spr round 13 (radius: 20)
[03:53:59 -158794.072750] SLOW spr round 14 (radius: 25)
[03:59:52 -158794.072734] Model parameter optimization (eps = 0.100000)

[04:00:01] ML tree search #4, logLikelihood: -158793.822624

[04:00:01 -1055258.777446] Initial branch length optimization
[04:00:05 -838677.807227] Model parameter optimization (eps = 10.000000)
[04:00:33 -837958.311921] AUTODETECT spr round 1 (radius: 5)
[04:02:39 -478549.466559] AUTODETECT spr round 2 (radius: 10)
[04:05:01 -317957.042655] AUTODETECT spr round 3 (radius: 15)
[04:07:13 -254548.078460] AUTODETECT spr round 4 (radius: 20)
[04:09:43 -216235.482652] AUTODETECT spr round 5 (radius: 25)
[04:12:34 -190808.568018] SPR radius for FAST iterations: 25 (autodetect)
[04:12:34 -190808.568018] Model parameter optimization (eps = 3.000000)
[04:12:53 -190541.914963] FAST spr round 1 (radius: 25)
[04:15:10 -160074.848551] FAST spr round 2 (radius: 25)
[04:16:55 -158972.292304] FAST spr round 3 (radius: 25)
[04:18:34 -158882.290609] FAST spr round 4 (radius: 25)
[04:20:10 -158824.099255] FAST spr round 5 (radius: 25)
[04:21:40 -158818.689391] FAST spr round 6 (radius: 25)
[04:23:08 -158818.689319] Model parameter optimization (eps = 1.000000)
[04:23:22 -158811.958063] SLOW spr round 1 (radius: 5)
[04:25:12 -158776.467851] SLOW spr round 2 (radius: 5)
[04:27:04 -158771.218041] SLOW spr round 3 (radius: 5)
[04:28:55 -158771.217851] SLOW spr round 4 (radius: 10)
[04:30:49 -158770.168728] SLOW spr round 5 (radius: 5)
[04:33:02 -158770.168597] SLOW spr round 6 (radius: 10)
[04:35:06 -158770.168553] SLOW spr round 7 (radius: 15)
[04:37:45 -158770.168337] SLOW spr round 8 (radius: 20)
[04:42:11 -158770.168319] SLOW spr round 9 (radius: 25)
[04:48:23 -158770.168300] Model parameter optimization (eps = 0.100000)

[04:48:28] ML tree search #5, logLikelihood: -158770.165200

[04:48:29 -1055485.597385] Initial branch length optimization
[04:48:32 -844538.612639] Model parameter optimization (eps = 10.000000)
[04:48:59 -843791.166922] AUTODETECT spr round 1 (radius: 5)
[04:51:08 -460227.882527] AUTODETECT spr round 2 (radius: 10)
[04:53:21 -312034.396565] AUTODETECT spr round 3 (radius: 15)
[04:55:43 -248935.801434] AUTODETECT spr round 4 (radius: 20)
[04:58:12 -217135.957646] AUTODETECT spr round 5 (radius: 25)
[05:00:56 -209734.820106] SPR radius for FAST iterations: 25 (autodetect)
[05:00:56 -209734.820106] Model parameter optimization (eps = 3.000000)
[05:01:16 -209395.435839] FAST spr round 1 (radius: 25)
[05:03:23 -169271.036714] FAST spr round 2 (radius: 25)
[05:05:11 -159704.425116] FAST spr round 3 (radius: 25)
[05:06:53 -158931.347911] FAST spr round 4 (radius: 25)
[05:08:30 -158890.217242] FAST spr round 5 (radius: 25)
[05:10:01 -158889.394200] FAST spr round 6 (radius: 25)
[05:11:30 -158889.394159] Model parameter optimization (eps = 1.000000)
[05:11:47 -158882.563422] SLOW spr round 1 (radius: 5)
[05:13:38 -158865.986420] SLOW spr round 2 (radius: 5)
[05:15:29 -158865.607337] SLOW spr round 3 (radius: 5)
[05:17:19 -158865.606788] SLOW spr round 4 (radius: 10)
[05:19:13 -158863.335059] SLOW spr round 5 (radius: 5)
[05:21:25 -158863.334858] SLOW spr round 6 (radius: 10)
[05:23:32 -158858.937336] SLOW spr round 7 (radius: 5)
[05:25:41 -158855.299184] SLOW spr round 8 (radius: 5)
[05:27:37 -158855.299117] SLOW spr round 9 (radius: 10)
[05:29:32 -158855.299062] SLOW spr round 10 (radius: 15)
[05:32:18 -158850.014645] SLOW spr round 11 (radius: 5)
[05:34:36 -158847.557584] SLOW spr round 12 (radius: 5)
[05:36:39 -158847.557490] SLOW spr round 13 (radius: 10)
[05:38:37 -158847.557475] SLOW spr round 14 (radius: 15)
[05:41:19 -158847.557460] SLOW spr round 15 (radius: 20)
[05:45:53 -158847.557445] SLOW spr round 16 (radius: 25)
[05:52:01 -158847.557429] Model parameter optimization (eps = 0.100000)

[05:52:10] ML tree search #6, logLikelihood: -158847.446348

[05:52:10 -1056028.289886] Initial branch length optimization
[05:52:14 -833746.790977] Model parameter optimization (eps = 10.000000)
[05:52:46 -833058.886493] AUTODETECT spr round 1 (radius: 5)
[05:54:51 -479862.445906] AUTODETECT spr round 2 (radius: 10)
[05:57:07 -329078.601793] AUTODETECT spr round 3 (radius: 15)
[05:59:26 -272180.221145] AUTODETECT spr round 4 (radius: 20)
[06:02:05 -223304.123199] AUTODETECT spr round 5 (radius: 25)
[06:05:07 -206842.195322] SPR radius for FAST iterations: 25 (autodetect)
[06:05:07 -206842.195322] Model parameter optimization (eps = 3.000000)
[06:05:34 -206528.424747] FAST spr round 1 (radius: 25)
[06:07:45 -161256.378852] FAST spr round 2 (radius: 25)
[06:09:37 -159244.447811] FAST spr round 3 (radius: 25)
[06:11:19 -159011.591768] FAST spr round 4 (radius: 25)
[06:12:55 -158942.781742] FAST spr round 5 (radius: 25)
[06:14:25 -158942.781284] Model parameter optimization (eps = 1.000000)
[06:14:41 -158935.420873] SLOW spr round 1 (radius: 5)
[06:16:33 -158907.784310] SLOW spr round 2 (radius: 5)
[06:18:25 -158903.413749] SLOW spr round 3 (radius: 5)
[06:20:17 -158902.728477] SLOW spr round 4 (radius: 5)
[06:22:08 -158901.778757] SLOW spr round 5 (radius: 5)
[06:23:57 -158901.778586] SLOW spr round 6 (radius: 10)
[06:25:51 -158896.497449] SLOW spr round 7 (radius: 5)
[06:28:09 -158876.695658] SLOW spr round 8 (radius: 5)
[06:30:09 -158875.474884] SLOW spr round 9 (radius: 5)
[06:32:02 -158875.474857] SLOW spr round 10 (radius: 10)
[06:33:57 -158856.396458] SLOW spr round 11 (radius: 5)
[06:36:08 -158856.396419] SLOW spr round 12 (radius: 10)
[06:38:12 -158856.396391] SLOW spr round 13 (radius: 15)
[06:40:58 -158843.262330] SLOW spr round 14 (radius: 5)
[06:43:18 -158840.775869] SLOW spr round 15 (radius: 5)
[06:45:23 -158840.775831] SLOW spr round 16 (radius: 10)
[06:47:20 -158840.775802] SLOW spr round 17 (radius: 15)
[06:50:09 -158840.775786] SLOW spr round 18 (radius: 20)
[06:54:55 -158840.775770] SLOW spr round 19 (radius: 25)
[07:01:24 -158840.775755] Model parameter optimization (eps = 0.100000)

[07:01:28] ML tree search #7, logLikelihood: -158840.769486

[07:01:28 -1059545.700195] Initial branch length optimization
[07:01:31 -843155.810575] Model parameter optimization (eps = 10.000000)
[07:02:08 -842469.129663] AUTODETECT spr round 1 (radius: 5)
[07:04:14 -470762.525968] AUTODETECT spr round 2 (radius: 10)
[07:06:32 -330205.561759] AUTODETECT spr round 3 (radius: 15)
[07:08:51 -251615.883354] AUTODETECT spr round 4 (radius: 20)
[07:11:31 -204658.169632] AUTODETECT spr round 5 (radius: 25)
[07:14:27 -196969.995523] SPR radius for FAST iterations: 25 (autodetect)
[07:14:27 -196969.995523] Model parameter optimization (eps = 3.000000)
[07:14:50 -196652.129799] FAST spr round 1 (radius: 25)
[07:17:03 -161651.518694] FAST spr round 2 (radius: 25)
[07:18:46 -158965.403330] FAST spr round 3 (radius: 25)
[07:20:25 -158848.228681] FAST spr round 4 (radius: 25)
[07:21:59 -158836.769928] FAST spr round 5 (radius: 25)
[07:23:28 -158836.769276] Model parameter optimization (eps = 1.000000)
[07:23:43 -158831.306784] SLOW spr round 1 (radius: 5)
[07:25:36 -158811.510987] SLOW spr round 2 (radius: 5)
[07:27:28 -158809.086447] SLOW spr round 3 (radius: 5)
[07:29:19 -158805.802795] SLOW spr round 4 (radius: 5)
[07:31:08 -158805.802684] SLOW spr round 5 (radius: 10)
[07:33:01 -158805.802672] SLOW spr round 6 (radius: 15)
[07:35:55 -158805.802469] SLOW spr round 7 (radius: 20)
[07:40:26 -158805.802464] SLOW spr round 8 (radius: 25)
[07:46:22 -158805.802458] Model parameter optimization (eps = 0.100000)

[07:46:29] ML tree search #8, logLikelihood: -158805.708367

[07:46:29 -1044212.115036] Initial branch length optimization
[07:46:32 -827799.988686] Model parameter optimization (eps = 10.000000)
[07:47:02 -827077.137147] AUTODETECT spr round 1 (radius: 5)
[07:49:08 -475610.305928] AUTODETECT spr round 2 (radius: 10)
[07:51:23 -332463.366935] AUTODETECT spr round 3 (radius: 15)
[07:53:49 -259669.141185] AUTODETECT spr round 4 (radius: 20)
[07:56:13 -216241.818936] AUTODETECT spr round 5 (radius: 25)
[07:58:49 -202571.228855] SPR radius for FAST iterations: 25 (autodetect)
[07:58:49 -202571.228855] Model parameter optimization (eps = 3.000000)
[07:59:10 -202241.072288] FAST spr round 1 (radius: 25)
[08:01:17 -164468.151873] FAST spr round 2 (radius: 25)
[08:03:03 -159121.926654] FAST spr round 3 (radius: 25)
[08:04:39 -158845.184982] FAST spr round 4 (radius: 25)
[08:06:17 -158830.116516] FAST spr round 5 (radius: 25)
[08:07:47 -158828.679097] FAST spr round 6 (radius: 25)
[08:09:15 -158828.678710] Model parameter optimization (eps = 1.000000)
[08:09:25 -158825.628248] SLOW spr round 1 (radius: 5)
[08:11:18 -158807.583051] SLOW spr round 2 (radius: 5)
[08:13:08 -158804.919826] SLOW spr round 3 (radius: 5)
[08:14:55 -158804.919389] SLOW spr round 4 (radius: 10)
[08:16:48 -158800.168127] SLOW spr round 5 (radius: 5)
[08:19:00 -158800.167567] SLOW spr round 6 (radius: 10)
[08:21:04 -158800.167556] SLOW spr round 7 (radius: 15)
[08:23:43 -158797.314024] SLOW spr round 8 (radius: 5)
[08:26:02 -158797.313570] SLOW spr round 9 (radius: 10)
[08:28:12 -158797.290911] SLOW spr round 10 (radius: 15)
[08:30:50 -158797.290900] SLOW spr round 11 (radius: 20)
[08:35:11 -158797.290889] SLOW spr round 12 (radius: 25)
[08:40:59 -158797.290878] Model parameter optimization (eps = 0.100000)

[08:41:04] ML tree search #9, logLikelihood: -158797.238441

[08:41:04 -1045229.704587] Initial branch length optimization
[08:41:08 -826993.751452] Model parameter optimization (eps = 10.000000)
[08:41:44 -826282.088750] AUTODETECT spr round 1 (radius: 5)
[08:43:52 -466438.010845] AUTODETECT spr round 2 (radius: 10)
[08:46:12 -312268.990112] AUTODETECT spr round 3 (radius: 15)
[08:48:38 -248704.370453] AUTODETECT spr round 4 (radius: 20)
[08:51:21 -202469.604233] AUTODETECT spr round 5 (radius: 25)
[08:54:18 -192255.387633] SPR radius for FAST iterations: 25 (autodetect)
[08:54:18 -192255.387633] Model parameter optimization (eps = 3.000000)
[08:54:41 -191992.755923] FAST spr round 1 (radius: 25)
[08:56:49 -161624.597318] FAST spr round 2 (radius: 25)
[08:58:32 -159015.854571] FAST spr round 3 (radius: 25)
[09:00:12 -158867.806265] FAST spr round 4 (radius: 25)
[09:01:46 -158854.039202] FAST spr round 5 (radius: 25)
[09:03:16 -158853.845165] FAST spr round 6 (radius: 25)
[09:04:44 -158853.845086] Model parameter optimization (eps = 1.000000)
[09:04:56 -158850.405208] SLOW spr round 1 (radius: 5)
[09:06:47 -158819.672440] SLOW spr round 2 (radius: 5)
[09:08:39 -158817.785771] SLOW spr round 3 (radius: 5)
[09:10:29 -158817.785517] SLOW spr round 4 (radius: 10)
[09:12:23 -158815.497841] SLOW spr round 5 (radius: 5)
[09:14:33 -158815.497336] SLOW spr round 6 (radius: 10)
[09:16:38 -158807.221696] SLOW spr round 7 (radius: 5)
[09:18:47 -158807.221252] SLOW spr round 8 (radius: 10)
[09:20:49 -158794.279454] SLOW spr round 9 (radius: 5)
[09:22:59 -158793.307867] SLOW spr round 10 (radius: 5)
[09:24:54 -158793.307818] SLOW spr round 11 (radius: 10)
[09:26:49 -158793.307806] SLOW spr round 12 (radius: 15)
[09:29:35 -158793.307793] SLOW spr round 13 (radius: 20)
[09:34:18 -158793.307781] SLOW spr round 14 (radius: 25)
[09:40:51 -158793.132500] SLOW spr round 15 (radius: 5)
[09:43:12 -158791.137002] SLOW spr round 16 (radius: 5)
[09:45:16 -158791.136940] SLOW spr round 17 (radius: 10)
[09:47:17 -158789.196382] SLOW spr round 18 (radius: 5)
[09:49:26 -158789.195562] SLOW spr round 19 (radius: 10)
[09:51:27 -158789.195520] SLOW spr round 20 (radius: 15)
[09:54:08 -158789.195494] SLOW spr round 21 (radius: 20)
[09:58:59 -158789.195474] SLOW spr round 22 (radius: 25)
[10:05:37 -158789.195458] Model parameter optimization (eps = 0.100000)

[10:05:45] ML tree search #10, logLikelihood: -158789.073870

[10:05:45 -1055267.292915] Initial branch length optimization
[10:05:49 -831462.375321] Model parameter optimization (eps = 10.000000)
[10:06:21 -830779.394936] AUTODETECT spr round 1 (radius: 5)
[10:08:31 -485305.632702] AUTODETECT spr round 2 (radius: 10)
[10:10:50 -318207.083907] AUTODETECT spr round 3 (radius: 15)
[10:13:05 -249527.190961] AUTODETECT spr round 4 (radius: 20)
[10:15:51 -209278.522596] AUTODETECT spr round 5 (radius: 25)
[10:18:57 -193838.354127] SPR radius for FAST iterations: 25 (autodetect)
[10:18:57 -193838.354127] Model parameter optimization (eps = 3.000000)
[10:19:22 -193470.803938] FAST spr round 1 (radius: 25)
[10:21:25 -160392.242481] FAST spr round 2 (radius: 25)
[10:23:09 -159027.402450] FAST spr round 3 (radius: 25)
[10:24:47 -158880.416549] FAST spr round 4 (radius: 25)
[10:26:22 -158835.002127] FAST spr round 5 (radius: 25)
[10:27:54 -158833.130997] FAST spr round 6 (radius: 25)
[10:29:23 -158833.130958] Model parameter optimization (eps = 1.000000)
[10:29:39 -158830.988155] SLOW spr round 1 (radius: 5)
[10:31:30 -158799.660406] SLOW spr round 2 (radius: 5)
[10:33:22 -158796.875131] SLOW spr round 3 (radius: 5)
[10:35:14 -158795.724868] SLOW spr round 4 (radius: 5)
[10:37:04 -158795.724649] SLOW spr round 5 (radius: 10)
[10:38:57 -158795.724627] SLOW spr round 6 (radius: 15)
[10:41:44 -158795.724606] SLOW spr round 7 (radius: 20)
[10:46:09 -158795.724585] SLOW spr round 8 (radius: 25)
[10:52:12 -158795.724564] Model parameter optimization (eps = 0.100000)

[10:52:22] ML tree search #11, logLikelihood: -158795.538350

[10:52:22 -1064861.429086] Initial branch length optimization
[10:52:25 -846417.551956] Model parameter optimization (eps = 10.000000)
[10:52:54 -845708.772208] AUTODETECT spr round 1 (radius: 5)
[10:55:01 -486516.931131] AUTODETECT spr round 2 (radius: 10)
[10:57:21 -325780.743365] AUTODETECT spr round 3 (radius: 15)
[10:59:38 -263738.193439] AUTODETECT spr round 4 (radius: 20)
[11:02:16 -224425.583299] AUTODETECT spr round 5 (radius: 25)
[11:05:18 -204408.818162] SPR radius for FAST iterations: 25 (autodetect)
[11:05:18 -204408.818162] Model parameter optimization (eps = 3.000000)
[11:05:46 -204083.689636] FAST spr round 1 (radius: 25)
[11:07:55 -165851.746135] FAST spr round 2 (radius: 25)
[11:09:41 -159279.847542] FAST spr round 3 (radius: 25)
[11:11:19 -158861.666922] FAST spr round 4 (radius: 25)
[11:12:56 -158846.012991] FAST spr round 5 (radius: 25)
[11:14:26 -158846.011708] Model parameter optimization (eps = 1.000000)
[11:14:41 -158840.318893] SLOW spr round 1 (radius: 5)
[11:16:31 -158820.373715] SLOW spr round 2 (radius: 5)
[11:18:23 -158814.222822] SLOW spr round 3 (radius: 5)
[11:20:14 -158814.222038] SLOW spr round 4 (radius: 10)
[11:22:09 -158814.221811] SLOW spr round 5 (radius: 15)
[11:24:57 -158814.221772] SLOW spr round 6 (radius: 20)
[11:29:25 -158814.221743] SLOW spr round 7 (radius: 25)
[11:35:49 -158814.221717] Model parameter optimization (eps = 0.100000)

[11:35:57] ML tree search #12, logLikelihood: -158814.109764

[11:35:58 -1042763.156403] Initial branch length optimization
[11:36:02 -830248.782057] Model parameter optimization (eps = 10.000000)
[11:36:27 -829550.747907] AUTODETECT spr round 1 (radius: 5)
[11:38:36 -469260.144829] AUTODETECT spr round 2 (radius: 10)
[11:40:57 -308795.240110] AUTODETECT spr round 3 (radius: 15)
[11:43:18 -253530.399769] AUTODETECT spr round 4 (radius: 20)
[11:45:52 -212707.594786] AUTODETECT spr round 5 (radius: 25)
[11:48:42 -201456.943201] SPR radius for FAST iterations: 25 (autodetect)
[11:48:42 -201456.943201] Model parameter optimization (eps = 3.000000)
[11:49:09 -201126.357761] FAST spr round 1 (radius: 25)
[11:51:18 -163770.069758] FAST spr round 2 (radius: 25)
[11:53:03 -159160.733981] FAST spr round 3 (radius: 25)
[11:54:41 -158844.173379] FAST spr round 4 (radius: 25)
[11:56:17 -158833.431362] FAST spr round 5 (radius: 25)
[11:57:49 -158823.094292] FAST spr round 6 (radius: 25)
[11:59:20 -158808.454902] FAST spr round 7 (radius: 25)
[12:00:49 -158808.454438] Model parameter optimization (eps = 1.000000)
[12:01:04 -158804.886605] SLOW spr round 1 (radius: 5)
[12:02:54 -158785.264498] SLOW spr round 2 (radius: 5)
[12:04:45 -158783.164731] SLOW spr round 3 (radius: 5)
[12:06:36 -158783.163023] SLOW spr round 4 (radius: 10)
[12:08:30 -158781.951068] SLOW spr round 5 (radius: 5)
[12:10:46 -158776.457714] SLOW spr round 6 (radius: 5)
[12:12:46 -158772.999745] SLOW spr round 7 (radius: 5)
[12:14:37 -158772.999650] SLOW spr round 8 (radius: 10)
[12:16:30 -158772.999610] SLOW spr round 9 (radius: 15)
[12:19:16 -158772.999598] SLOW spr round 10 (radius: 20)
[12:23:39 -158772.999585] SLOW spr round 11 (radius: 25)
[12:29:22 -158772.999573] Model parameter optimization (eps = 0.100000)

[12:29:29] ML tree search #13, logLikelihood: -158772.926581

[12:29:29 -1049838.081778] Initial branch length optimization
[12:29:33 -837017.118808] Model parameter optimization (eps = 10.000000)
[12:30:07 -836279.906444] AUTODETECT spr round 1 (radius: 5)
[12:32:14 -472476.054285] AUTODETECT spr round 2 (radius: 10)
[12:34:24 -312538.231837] AUTODETECT spr round 3 (radius: 15)
[12:36:46 -238004.057049] AUTODETECT spr round 4 (radius: 20)
[12:39:18 -199744.786457] AUTODETECT spr round 5 (radius: 25)
[12:42:11 -194759.118985] SPR radius for FAST iterations: 25 (autodetect)
[12:42:11 -194759.118985] Model parameter optimization (eps = 3.000000)
[12:42:44 -194457.028252] FAST spr round 1 (radius: 25)
[12:44:56 -162255.205173] FAST spr round 2 (radius: 25)
[12:46:47 -159132.717072] FAST spr round 3 (radius: 25)
[12:48:26 -158928.835632] FAST spr round 4 (radius: 25)
[12:50:00 -158903.679556] FAST spr round 5 (radius: 25)
[12:51:29 -158903.679193] Model parameter optimization (eps = 1.000000)
[12:51:42 -158901.110877] SLOW spr round 1 (radius: 5)
[12:53:31 -158875.071840] SLOW spr round 2 (radius: 5)
[12:55:22 -158868.417962] SLOW spr round 3 (radius: 5)
[12:57:13 -158867.222724] SLOW spr round 4 (radius: 5)
[12:59:01 -158867.222445] SLOW spr round 5 (radius: 10)
[13:00:55 -158865.606017] SLOW spr round 6 (radius: 5)
[13:03:07 -158865.605872] SLOW spr round 7 (radius: 10)
[13:05:11 -158865.605830] SLOW spr round 8 (radius: 15)
[13:07:48 -158862.859644] SLOW spr round 9 (radius: 5)
[13:10:07 -158862.164753] SLOW spr round 10 (radius: 5)
[13:12:10 -158862.164686] SLOW spr round 11 (radius: 10)
[13:14:07 -158862.164645] SLOW spr round 12 (radius: 15)
[13:16:48 -158862.164630] SLOW spr round 13 (radius: 20)
[13:20:58 -158862.164615] SLOW spr round 14 (radius: 25)
[13:26:43 -158862.164599] Model parameter optimization (eps = 0.100000)

[13:26:53] ML tree search #14, logLikelihood: -158861.949155

[13:26:53 -1050647.076912] Initial branch length optimization
[13:26:57 -834016.655649] Model parameter optimization (eps = 10.000000)
[13:27:33 -833299.182529] AUTODETECT spr round 1 (radius: 5)
[13:29:41 -462098.377591] AUTODETECT spr round 2 (radius: 10)
[13:31:55 -316544.106958] AUTODETECT spr round 3 (radius: 15)
[13:34:15 -253610.314624] AUTODETECT spr round 4 (radius: 20)
[13:36:48 -222196.073069] AUTODETECT spr round 5 (radius: 25)
[13:40:43 -204264.582026] SPR radius for FAST iterations: 25 (autodetect)
[13:40:43 -204264.582026] Model parameter optimization (eps = 3.000000)
[13:41:11 -203891.937966] FAST spr round 1 (radius: 25)
[13:43:22 -161288.437444] FAST spr round 2 (radius: 25)
[13:45:11 -158950.615537] FAST spr round 3 (radius: 25)
[13:46:50 -158844.725297] FAST spr round 4 (radius: 25)
[13:48:23 -158816.738213] FAST spr round 5 (radius: 25)
[13:49:52 -158815.767684] FAST spr round 6 (radius: 25)
[13:51:20 -158815.767648] Model parameter optimization (eps = 1.000000)
[13:51:33 -158811.646218] SLOW spr round 1 (radius: 5)
[13:53:22 -158797.866781] SLOW spr round 2 (radius: 5)
[13:55:12 -158793.404546] SLOW spr round 3 (radius: 5)
[13:57:03 -158789.785194] SLOW spr round 4 (radius: 5)
[13:58:51 -158789.785025] SLOW spr round 5 (radius: 10)
[14:00:43 -158789.778547] SLOW spr round 6 (radius: 15)
[14:03:36 -158789.778337] SLOW spr round 7 (radius: 20)
[14:08:08 -158789.778326] SLOW spr round 8 (radius: 25)
[14:14:21 -158789.778314] Model parameter optimization (eps = 0.100000)

[14:14:26] ML tree search #15, logLikelihood: -158789.748704

[14:14:26 -1062195.462810] Initial branch length optimization
[14:14:29 -844403.426114] Model parameter optimization (eps = 10.000000)
[14:14:57 -843643.026809] AUTODETECT spr round 1 (radius: 5)
[14:17:06 -481354.997821] AUTODETECT spr round 2 (radius: 10)
[14:19:24 -304802.709920] AUTODETECT spr round 3 (radius: 15)
[14:21:43 -255226.201712] AUTODETECT spr round 4 (radius: 20)
[14:24:14 -222191.462629] AUTODETECT spr round 5 (radius: 25)
[14:27:16 -202024.040674] SPR radius for FAST iterations: 25 (autodetect)
[14:27:16 -202024.040674] Model parameter optimization (eps = 3.000000)
[14:27:40 -201725.939132] FAST spr round 1 (radius: 25)
[14:29:53 -161162.658777] FAST spr round 2 (radius: 25)
[14:31:47 -158959.104075] FAST spr round 3 (radius: 25)
[14:33:29 -158840.934992] FAST spr round 4 (radius: 25)
[14:35:03 -158827.136900] FAST spr round 5 (radius: 25)
[14:36:34 -158826.325463] FAST spr round 6 (radius: 25)
[14:38:03 -158826.325440] Model parameter optimization (eps = 1.000000)
[14:38:17 -158822.217818] SLOW spr round 1 (radius: 5)
[14:40:08 -158807.697473] SLOW spr round 2 (radius: 5)
[14:42:00 -158806.478599] SLOW spr round 3 (radius: 5)
[14:43:52 -158806.474321] SLOW spr round 4 (radius: 10)
[14:45:49 -158798.585037] SLOW spr round 5 (radius: 5)
[14:48:03 -158797.557132] SLOW spr round 6 (radius: 5)
[14:50:03 -158794.263715] SLOW spr round 7 (radius: 5)
[14:51:54 -158794.263679] SLOW spr round 8 (radius: 10)
[14:53:48 -158794.263597] SLOW spr round 9 (radius: 15)
[14:56:40 -158794.263584] SLOW spr round 10 (radius: 20)
[15:01:28 -158794.263572] SLOW spr round 11 (radius: 25)
[15:08:08 -158794.263560] Model parameter optimization (eps = 0.100000)

[15:08:15] ML tree search #16, logLikelihood: -158794.199360

[15:08:15 -1057729.854860] Initial branch length optimization
[15:08:20 -832303.941660] Model parameter optimization (eps = 10.000000)
[15:08:47 -831574.372453] AUTODETECT spr round 1 (radius: 5)
[15:10:55 -469256.318788] AUTODETECT spr round 2 (radius: 10)
[15:13:08 -312754.939910] AUTODETECT spr round 3 (radius: 15)
[15:15:25 -241848.936243] AUTODETECT spr round 4 (radius: 20)
[15:17:52 -216702.022579] AUTODETECT spr round 5 (radius: 25)
[15:20:34 -196396.857772] SPR radius for FAST iterations: 25 (autodetect)
[15:20:35 -196396.857772] Model parameter optimization (eps = 3.000000)
[15:20:59 -196091.115112] FAST spr round 1 (radius: 25)
[15:23:09 -163984.627828] FAST spr round 2 (radius: 25)
[15:25:01 -160747.172877] FAST spr round 3 (radius: 25)
[15:26:43 -159080.329941] FAST spr round 4 (radius: 25)
[15:28:21 -158841.388500] FAST spr round 5 (radius: 25)
[15:29:55 -158831.483264] FAST spr round 6 (radius: 25)
[15:31:27 -158828.482910] FAST spr round 7 (radius: 25)
[15:32:59 -158828.482586] Model parameter optimization (eps = 1.000000)
[15:33:14 -158824.576572] SLOW spr round 1 (radius: 5)
[15:35:07 -158785.745772] SLOW spr round 2 (radius: 5)
[15:37:01 -158784.313902] SLOW spr round 3 (radius: 5)
[15:38:54 -158784.312888] SLOW spr round 4 (radius: 10)
[15:40:49 -158784.312391] SLOW spr round 5 (radius: 15)
[15:43:33 -158784.312372] SLOW spr round 6 (radius: 20)
[15:47:42 -158784.312354] SLOW spr round 7 (radius: 25)
[15:53:11 -158784.312335] Model parameter optimization (eps = 0.100000)

[15:53:21] ML tree search #17, logLikelihood: -158784.163900

[15:53:22 -1041647.161949] Initial branch length optimization
[15:53:25 -824916.510600] Model parameter optimization (eps = 10.000000)
[15:53:52 -824179.755424] AUTODETECT spr round 1 (radius: 5)
[15:55:59 -485511.756199] AUTODETECT spr round 2 (radius: 10)
[15:58:20 -339150.678832] AUTODETECT spr round 3 (radius: 15)
[16:00:41 -273282.652297] AUTODETECT spr round 4 (radius: 20)
[16:03:19 -231474.597820] AUTODETECT spr round 5 (radius: 25)
[16:06:11 -213163.470932] SPR radius for FAST iterations: 25 (autodetect)
[16:06:11 -213163.470932] Model parameter optimization (eps = 3.000000)
[16:06:34 -212849.989754] FAST spr round 1 (radius: 25)
[16:08:47 -165824.416205] FAST spr round 2 (radius: 25)
[16:10:35 -159585.029253] FAST spr round 3 (radius: 25)
[16:12:16 -158927.846812] FAST spr round 4 (radius: 25)
[16:13:53 -158896.312213] FAST spr round 5 (radius: 25)
[16:15:28 -158811.127950] FAST spr round 6 (radius: 25)
[16:16:58 -158811.127602] Model parameter optimization (eps = 1.000000)
[16:17:11 -158805.772200] SLOW spr round 1 (radius: 5)
[16:19:02 -158781.917974] SLOW spr round 2 (radius: 5)
[16:20:53 -158781.914562] SLOW spr round 3 (radius: 10)
[16:22:50 -158780.866309] SLOW spr round 4 (radius: 5)
[16:25:06 -158780.865535] SLOW spr round 5 (radius: 10)
[16:27:11 -158780.865484] SLOW spr round 6 (radius: 15)
[16:29:52 -158780.178485] SLOW spr round 7 (radius: 5)
[16:32:14 -158772.352891] SLOW spr round 8 (radius: 5)
[16:34:18 -158772.352835] SLOW spr round 9 (radius: 10)
[16:36:16 -158772.352818] SLOW spr round 10 (radius: 15)
[16:39:01 -158772.352802] SLOW spr round 11 (radius: 20)
[16:43:27 -158772.352785] SLOW spr round 12 (radius: 25)
[16:49:11 -158772.352769] Model parameter optimization (eps = 0.100000)

[16:49:15] ML tree search #18, logLikelihood: -158772.330619

[16:49:15 -1060215.629568] Initial branch length optimization
[16:49:19 -837948.473126] Model parameter optimization (eps = 10.000000)
[16:49:48 -837228.167723] AUTODETECT spr round 1 (radius: 5)
[16:51:58 -485588.466756] AUTODETECT spr round 2 (radius: 10)
[16:54:19 -326346.444386] AUTODETECT spr round 3 (radius: 15)
[16:56:41 -246626.679057] AUTODETECT spr round 4 (radius: 20)
[16:59:09 -200740.631722] AUTODETECT spr round 5 (radius: 25)
[17:02:12 -188561.782998] SPR radius for FAST iterations: 25 (autodetect)
[17:02:12 -188561.782998] Model parameter optimization (eps = 3.000000)
[17:02:37 -188278.564771] FAST spr round 1 (radius: 25)
[17:04:45 -160277.257485] FAST spr round 2 (radius: 25)
[17:06:32 -158979.391250] FAST spr round 3 (radius: 25)
[17:08:12 -158914.919260] FAST spr round 4 (radius: 25)
[17:09:48 -158875.203092] FAST spr round 5 (radius: 25)
[17:11:19 -158875.201702] Model parameter optimization (eps = 1.000000)
[17:11:34 -158869.126055] SLOW spr round 1 (radius: 5)
[17:13:28 -158832.853131] SLOW spr round 2 (radius: 5)
[17:15:20 -158828.768912] SLOW spr round 3 (radius: 5)
[17:17:10 -158828.768513] SLOW spr round 4 (radius: 10)
[17:19:04 -158828.768402] SLOW spr round 5 (radius: 15)
[17:21:56 -158828.768340] SLOW spr round 6 (radius: 20)
[17:26:22 -158828.768284] SLOW spr round 7 (radius: 25)
[17:32:24 -158828.768230] Model parameter optimization (eps = 0.100000)

[17:32:29] ML tree search #19, logLikelihood: -158828.722184

[17:32:29 -1052819.569544] Initial branch length optimization
[17:32:33 -829282.544660] Model parameter optimization (eps = 10.000000)
[17:32:59 -828563.608761] AUTODETECT spr round 1 (radius: 5)
[17:35:06 -496350.306134] AUTODETECT spr round 2 (radius: 10)
[17:37:27 -330517.606826] AUTODETECT spr round 3 (radius: 15)
[17:39:48 -270587.611375] AUTODETECT spr round 4 (radius: 20)
[17:42:36 -203854.901348] AUTODETECT spr round 5 (radius: 25)
[17:45:07 -195152.371492] SPR radius for FAST iterations: 25 (autodetect)
[17:45:07 -195152.371492] Model parameter optimization (eps = 3.000000)
[17:45:38 -194829.173230] FAST spr round 1 (radius: 25)
[17:47:44 -160312.760702] FAST spr round 2 (radius: 25)
[17:49:30 -158989.268846] FAST spr round 3 (radius: 25)
[17:51:10 -158869.480525] FAST spr round 4 (radius: 25)
[17:52:44 -158844.606684] FAST spr round 5 (radius: 25)
[17:54:17 -158829.254446] FAST spr round 6 (radius: 25)
[17:55:46 -158829.254329] Model parameter optimization (eps = 1.000000)
[17:56:02 -158823.345559] SLOW spr round 1 (radius: 5)
[17:57:53 -158798.131821] SLOW spr round 2 (radius: 5)
[17:59:44 -158796.252049] SLOW spr round 3 (radius: 5)
[18:01:35 -158793.484309] SLOW spr round 4 (radius: 5)
[18:03:24 -158793.484177] SLOW spr round 5 (radius: 10)
[18:05:16 -158791.013918] SLOW spr round 6 (radius: 5)
[18:07:28 -158791.013868] SLOW spr round 7 (radius: 10)
[18:09:32 -158791.013853] SLOW spr round 8 (radius: 15)
[18:12:14 -158791.013838] SLOW spr round 9 (radius: 20)
[18:16:54 -158791.013823] SLOW spr round 10 (radius: 25)
[18:23:02 -158791.013809] Model parameter optimization (eps = 0.100000)

[18:23:09] ML tree search #20, logLikelihood: -158790.923169


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.217238,0.311279) (0.219842,0.465670) (0.373338,1.014451) (0.189581,2.380357) 
   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: -158751.414980

AIC score: 321512.829959 / AICc score: 8365572.829959 / BIC score: 330754.575192
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=742).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 307 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P48058/3_mltree/P48058.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P48058/3_mltree/P48058.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P48058/3_mltree/P48058.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P48058/3_mltree/P48058.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P48058/3_mltree/P48058.raxml.log

Analysis started: 30-Jun-2021 17:09:07 / finished: 01-Jul-2021 11:32:16

Elapsed time: 66189.541 seconds