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 04-Jul-2021 02:23:22 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9HCR9/2_msa/Q9HCR9_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9HCR9/3_mltree/Q9HCR9 --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/Q9HCR9/2_msa/Q9HCR9_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 612 sites

WARNING: Sequences tr_B4Q8U9_B4Q8U9_DROSI_7240 and tr_B4I5H6_B4I5H6_DROSE_7238 are exactly identical!
WARNING: Sequences sp_B4QZU1_PDE6_DROSI_7240 and sp_Q9VFI9_PDE6_DROME_7227 are exactly identical!
WARNING: Sequences sp_B4QZU1_PDE6_DROSI_7240 and sp_B4HEM4_PDE6_DROSE_7238 are exactly identical!
WARNING: Sequences tr_F7D3W5_F7D3W5_MOUSE_10090 and sp_Q922S4_PDE2A_MOUSE_10090 are exactly identical!
WARNING: Sequences tr_M3Z148_M3Z148_MUSPF_9669 and tr_A0A2Y9K5W1_A0A2Y9K5W1_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A2I2YX44_A0A2I2YX44_GORGO_9595 and tr_H2PKU2_H2PKU2_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I2YX44_A0A2I2YX44_GORGO_9595 and sp_Q9Y233_PDE10_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G1NIA7_G1NIA7_MELGA_9103 and tr_U3IPQ8_U3IPQ8_ANAPL_8839 are exactly identical!
WARNING: Sequences tr_G1NIA7_G1NIA7_MELGA_9103 and tr_A0A091JNW8_A0A091JNW8_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_G1NIA7_G1NIA7_MELGA_9103 and tr_A0A091UL34_A0A091UL34_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_G1NIA7_G1NIA7_MELGA_9103 and tr_A0A087R0D5_A0A087R0D5_APTFO_9233 are exactly identical!
WARNING: Sequences tr_G1NIA7_G1NIA7_MELGA_9103 and tr_A0A0A0AV41_A0A0A0AV41_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_G1NIA7_G1NIA7_MELGA_9103 and tr_A0A093GH96_A0A093GH96_DRYPU_118200 are exactly identical!
WARNING: Sequences sp_Q298P4_PDE6_DROPS_46245 and sp_B4G4E5_PDE6_DROPE_7234 are exactly identical!
WARNING: Sequences tr_A0A0A0MPD7_A0A0A0MPD7_CANLF_9615 and sp_Q28263_PDE6A_CANLF_9615 are exactly identical!
WARNING: Sequences tr_A0A2I3SBR0_A0A2I3SBR0_PANTR_9598 and tr_A0A2R9B3Z4_A0A2R9B3Z4_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QRS3_H2QRS3_PANTR_9598 and tr_A0A2R8ZUN2_A0A2R8ZUN2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2R206_H2R206_PANTR_9598 and tr_A0A2R9CF87_A0A2R9CF87_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2R546_H2R546_PANTR_9598 and sp_O00408_PDE2A_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2R546_H2R546_PANTR_9598 and tr_A0A2R9BH84_A0A2R9BH84_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A088ADF4_A0A088ADF4_APIME_7460 and tr_A0A2A3EEB7_A0A2A3EEB7_APICC_94128 are exactly identical!
WARNING: Sequences tr_A0A158NVJ1_A0A158NVJ1_ATTCE_12957 and tr_A0A195BPH2_A0A195BPH2_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A1D5QMF7_A0A1D5QMF7_MACMU_9544 and tr_G7P485_G7P485_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5QMF7_A0A1D5QMF7_MACMU_9544 and tr_A0A2I3N0I6_A0A2I3N0I6_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5QMF7_A0A1D5QMF7_MACMU_9544 and tr_A0A2K6B761_A0A2K6B761_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5R2R1_A0A1D5R2R1_MACMU_9544 and tr_G7PDK9_G7PDK9_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A1D5R2R1_A0A1D5R2R1_MACMU_9544 and tr_A0A096P5N5_A0A096P5N5_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5R2R1_A0A1D5R2R1_MACMU_9544 and tr_A0A0D9R1P5_A0A0D9R1P5_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A1D5R2R1_A0A1D5R2R1_MACMU_9544 and tr_A0A2K5LDX2_A0A2K5LDX2_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5R2R1_A0A1D5R2R1_MACMU_9544 and tr_A0A2K6DHH9_A0A2K6DHH9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6SMY5_F6SMY5_MACMU_9544 and tr_G7P8N7_G7P8N7_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6SMY5_F6SMY5_MACMU_9544 and tr_A0A2K6E284_A0A2K6E284_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6TL18_F6TL18_MACMU_9544 and tr_A0A2K6AXL5_A0A2K6AXL5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_H0ZGL6_H0ZGL6_TAEGU_59729 and tr_U3KCJ2_U3KCJ2_FICAL_59894 are exactly identical!
WARNING: Sequences tr_G7P667_G7P667_MACFA_9541 and tr_A0A096NYB4_A0A096NYB4_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7P667_G7P667_MACFA_9541 and tr_A0A0D9QUR9_A0A0D9QUR9_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G7P667_G7P667_MACFA_9541 and tr_A0A2K5LKX0_A0A2K5LKX0_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7P667_G7P667_MACFA_9541 and tr_A0A2K6AWP5_A0A2K6AWP5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7P667_G7P667_MACFA_9541 and tr_A0A2K5YPY9_A0A2K5YPY9_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096NDS5_A0A096NDS5_PAPAN_9555 and tr_A0A0D9RP45_A0A0D9RP45_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A096NDS5_A0A096NDS5_PAPAN_9555 and tr_A0A2K6AKE7_A0A2K6AKE7_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A151MM47_A0A151MM47_ALLMI_8496 and tr_A0A1U8DU20_A0A1U8DU20_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A0V1D6N6_A0A0V1D6N6_TRIBR_45882 and tr_A0A0V1P9M7_A0A0V1P9M7_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A2D0QKM7_A0A2D0QKM7_ICTPU_7998 and tr_A0A2D0QKY9_A0A2D0QKY9_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QKM7_A0A2D0QKM7_ICTPU_7998 and tr_A0A2D0QN85_A0A2D0QN85_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QKM7_A0A2D0QKM7_ICTPU_7998 and tr_W6A375_W6A375_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RCQ8_A0A2D0RCQ8_ICTPU_7998 and tr_A0A2D0RCR1_A0A2D0RCR1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RCQ8_A0A2D0RCQ8_ICTPU_7998 and tr_A0A2D0RCR4_A0A2D0RCR4_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0T1G7_A0A2D0T1G7_ICTPU_7998 and tr_A0A2D0T1H4_A0A2D0T1H4_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2K5L3C7_A0A2K5L3C7_CERAT_9531 and tr_A0A2K5Z480_A0A2K5Z480_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2K5N3W7_A0A2K5N3W7_CERAT_9531 and tr_A0A2K5ZB20_A0A2K5ZB20_MANLE_9568 are exactly identical!
WARNING: Duplicate sequences found: 51

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/Q9HCR9/3_mltree/Q9HCR9.raxml.reduced.phy

Alignment comprises 1 partitions and 612 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 612 / 612
Gaps: 8.73 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9HCR9/3_mltree/Q9HCR9.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 / 88 / 7040
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1072978.940700] Initial branch length optimization
[00:00:06 -887288.971873] Model parameter optimization (eps = 10.000000)
[00:08:08 -883655.968931] AUTODETECT spr round 1 (radius: 5)
[01:16:56 -505690.530877] AUTODETECT spr round 2 (radius: 10)
[03:06:56 -358973.353607] AUTODETECT spr round 3 (radius: 15)
[04:32:12 -288960.703946] AUTODETECT spr round 4 (radius: 20)
[04:34:29 -252920.892230] AUTODETECT spr round 5 (radius: 25)
[04:37:12 -243864.192470] SPR radius for FAST iterations: 25 (autodetect)
[04:37:12 -243864.192470] Model parameter optimization (eps = 3.000000)
[04:37:32 -243672.263831] FAST spr round 1 (radius: 25)
[05:18:21 -208495.573956] FAST spr round 2 (radius: 25)
[05:20:27 -206809.834768] FAST spr round 3 (radius: 25)
[05:30:52 -206718.704276] FAST spr round 4 (radius: 25)
[05:37:13 -206712.685617] FAST spr round 5 (radius: 25)
[05:39:03 -206712.282012] FAST spr round 6 (radius: 25)
[05:41:13 -206712.281329] Model parameter optimization (eps = 1.000000)
[05:41:20 -206711.367141] SLOW spr round 1 (radius: 5)
[05:43:31 -206674.261627] SLOW spr round 2 (radius: 5)
[05:51:04 -206664.626262] SLOW spr round 3 (radius: 5)
[06:05:33 -206664.625484] SLOW spr round 4 (radius: 10)
[06:07:33 -206662.676912] SLOW spr round 5 (radius: 5)
[06:10:00 -206661.980690] SLOW spr round 6 (radius: 5)
[06:12:10 -206661.980564] SLOW spr round 7 (radius: 10)
[06:14:16 -206661.980459] SLOW spr round 8 (radius: 15)
[06:17:02 -206661.980367] SLOW spr round 9 (radius: 20)
[06:39:30 -206661.980286] SLOW spr round 10 (radius: 25)
[06:53:48 -206661.980215] Model parameter optimization (eps = 0.100000)

[06:56:20] ML tree search #1, logLikelihood: -206661.819526

[06:56:21 -1066451.774250] Initial branch length optimization
[06:56:26 -879189.572909] Model parameter optimization (eps = 10.000000)
[06:58:46 -875732.631594] AUTODETECT spr round 1 (radius: 5)
[07:10:01 -526516.283743] AUTODETECT spr round 2 (radius: 10)
[07:13:45 -380100.425293] AUTODETECT spr round 3 (radius: 15)
[08:12:01 -314991.195762] AUTODETECT spr round 4 (radius: 20)
[08:14:54 -257226.127927] AUTODETECT spr round 5 (radius: 25)
[08:50:14 -249030.047852] SPR radius for FAST iterations: 25 (autodetect)
[08:50:14 -249030.047852] Model parameter optimization (eps = 3.000000)
[08:50:36 -248885.080762] FAST spr round 1 (radius: 25)
[09:02:24 -209077.421749] FAST spr round 2 (radius: 25)
[09:05:20 -206874.725183] FAST spr round 3 (radius: 25)
[09:18:31 -206731.506674] FAST spr round 4 (radius: 25)
[09:23:53 -206711.516082] FAST spr round 5 (radius: 25)
[09:35:03 -206707.702314] FAST spr round 6 (radius: 25)
[09:36:48 -206707.702286] Model parameter optimization (eps = 1.000000)
[09:37:06 -206706.502009] SLOW spr round 1 (radius: 5)
[09:40:30 -206667.604439] SLOW spr round 2 (radius: 5)
[09:43:00 -206661.792408] SLOW spr round 3 (radius: 5)
[11:25:11 -206661.027975] SLOW spr round 4 (radius: 5)
[11:27:23 -206661.027953] SLOW spr round 5 (radius: 10)
[11:29:33 -206660.845115] SLOW spr round 6 (radius: 5)
[11:46:35 -206659.303536] SLOW spr round 7 (radius: 5)
[12:27:53 -206659.303506] SLOW spr round 8 (radius: 10)
[12:40:21 -206659.303499] SLOW spr round 9 (radius: 15)
[13:39:18 -206659.303493] SLOW spr round 10 (radius: 20)
[17:11:29 -206659.303489] SLOW spr round 11 (radius: 25)
[24:56:52 -206659.303484] Model parameter optimization (eps = 0.100000)

[24:56:59] ML tree search #2, logLikelihood: -206659.199725

[24:56:59 -1074385.501895] Initial branch length optimization
[24:57:03 -891349.380952] Model parameter optimization (eps = 10.000000)
[24:57:45 -887501.942781] AUTODETECT spr round 1 (radius: 5)
[24:59:48 -510245.575350] AUTODETECT spr round 2 (radius: 10)
[25:01:58 -374264.140150] AUTODETECT spr round 3 (radius: 15)
[25:04:30 -304283.081578] AUTODETECT spr round 4 (radius: 20)
[25:07:10 -256882.230850] AUTODETECT spr round 5 (radius: 25)
[25:10:07 -242109.210315] SPR radius for FAST iterations: 25 (autodetect)
[25:10:07 -242109.210315] Model parameter optimization (eps = 3.000000)
[25:10:28 -241961.949082] FAST spr round 1 (radius: 25)
[25:12:53 -208096.143349] FAST spr round 2 (radius: 25)
[25:14:49 -206781.426237] FAST spr round 3 (radius: 25)
[25:16:42 -206721.822311] FAST spr round 4 (radius: 25)
[25:18:21 -206721.821269] Model parameter optimization (eps = 1.000000)
[25:18:35 -206718.540044] SLOW spr round 1 (radius: 5)
[25:20:49 -206674.929208] SLOW spr round 2 (radius: 5)
[25:22:58 -206667.338159] SLOW spr round 3 (radius: 5)
[25:25:01 -206667.201179] SLOW spr round 4 (radius: 5)
[25:27:04 -206667.201140] SLOW spr round 5 (radius: 10)
[25:29:08 -206666.032710] SLOW spr round 6 (radius: 5)
[25:31:35 -206663.908990] SLOW spr round 7 (radius: 5)
[25:33:48 -206663.908949] SLOW spr round 8 (radius: 10)
[25:35:55 -206663.908942] SLOW spr round 9 (radius: 15)
[25:38:43 -206663.908935] SLOW spr round 10 (radius: 20)
[25:43:04 -206663.908929] SLOW spr round 11 (radius: 25)
[25:48:43 -206663.526756] SLOW spr round 12 (radius: 5)
[25:51:18 -206663.385286] SLOW spr round 13 (radius: 5)
[25:53:36 -206663.384749] SLOW spr round 14 (radius: 10)
[25:55:46 -206663.384744] SLOW spr round 15 (radius: 15)
[25:58:31 -206663.384739] SLOW spr round 16 (radius: 20)
[26:02:51 -206663.384734] SLOW spr round 17 (radius: 25)
[26:08:28 -206663.384729] Model parameter optimization (eps = 0.100000)

[26:08:35] ML tree search #3, logLikelihood: -206663.278638

[26:08:35 -1076612.184684] Initial branch length optimization
[26:08:40 -891425.888520] Model parameter optimization (eps = 10.000000)
[26:09:09 -887883.968154] AUTODETECT spr round 1 (radius: 5)
[26:11:10 -511611.881175] AUTODETECT spr round 2 (radius: 10)
[26:13:19 -358333.406409] AUTODETECT spr round 3 (radius: 15)
[26:15:36 -276297.233521] AUTODETECT spr round 4 (radius: 20)
[26:18:06 -239670.769898] AUTODETECT spr round 5 (radius: 25)
[26:21:09 -235184.629383] SPR radius for FAST iterations: 25 (autodetect)
[26:21:09 -235184.629383] Model parameter optimization (eps = 3.000000)
[26:21:34 -235018.979843] FAST spr round 1 (radius: 25)
[26:24:45 -207685.257155] FAST spr round 2 (radius: 25)
[26:26:48 -206817.477569] FAST spr round 3 (radius: 25)
[26:28:38 -206756.022528] FAST spr round 4 (radius: 25)
[26:30:21 -206751.087819] FAST spr round 5 (radius: 25)
[26:31:59 -206751.087468] Model parameter optimization (eps = 1.000000)
[26:32:15 -206749.386086] SLOW spr round 1 (radius: 5)
[26:34:26 -206675.957880] SLOW spr round 2 (radius: 5)
[26:36:34 -206668.140069] SLOW spr round 3 (radius: 5)
[26:38:37 -206665.917765] SLOW spr round 4 (radius: 5)
[26:40:38 -206664.574221] SLOW spr round 5 (radius: 5)
[26:42:40 -206664.573607] SLOW spr round 6 (radius: 10)
[26:44:42 -206664.573484] SLOW spr round 7 (radius: 15)
[26:47:38 -206664.351077] SLOW spr round 8 (radius: 5)
[26:50:14 -206662.233139] SLOW spr round 9 (radius: 5)
[26:52:33 -206662.232508] SLOW spr round 10 (radius: 10)
[26:54:46 -206662.232497] SLOW spr round 11 (radius: 15)
[26:57:36 -206662.232486] SLOW spr round 12 (radius: 20)
[27:01:52 -206662.232476] SLOW spr round 13 (radius: 25)
[27:07:27 -206660.033326] SLOW spr round 14 (radius: 5)
[27:10:01 -206659.233996] SLOW spr round 15 (radius: 5)
[27:12:19 -206659.233971] SLOW spr round 16 (radius: 10)
[27:14:29 -206659.233962] SLOW spr round 17 (radius: 15)
[27:17:15 -206659.233955] SLOW spr round 18 (radius: 20)
[27:21:32 -206659.233947] SLOW spr round 19 (radius: 25)
[27:27:03 -206659.233940] Model parameter optimization (eps = 0.100000)

[27:27:15] ML tree search #4, logLikelihood: -206658.722285

[27:27:15 -1070101.580651] Initial branch length optimization
[27:27:19 -888518.562324] Model parameter optimization (eps = 10.000000)
[27:27:51 -884886.517561] AUTODETECT spr round 1 (radius: 5)
[27:29:52 -496276.708765] AUTODETECT spr round 2 (radius: 10)
[27:32:01 -360562.605619] AUTODETECT spr round 3 (radius: 15)
[27:34:13 -305903.377471] AUTODETECT spr round 4 (radius: 20)
[27:36:47 -266749.467661] AUTODETECT spr round 5 (radius: 25)
[27:39:55 -251946.377191] SPR radius for FAST iterations: 25 (autodetect)
[27:39:55 -251946.377191] Model parameter optimization (eps = 3.000000)
[27:40:21 -251809.056335] FAST spr round 1 (radius: 25)
[27:42:51 -208215.101162] FAST spr round 2 (radius: 25)
[27:44:57 -206823.115525] FAST spr round 3 (radius: 25)
[27:47:24 -206722.585054] FAST spr round 4 (radius: 25)
[27:49:57 -206719.832594] FAST spr round 5 (radius: 25)
[27:51:36 -206718.088233] FAST spr round 6 (radius: 25)
[27:53:16 -206718.087219] Model parameter optimization (eps = 1.000000)
[27:53:31 -206711.643984] SLOW spr round 1 (radius: 5)
[27:55:40 -206666.875607] SLOW spr round 2 (radius: 5)
[27:57:47 -206656.879723] SLOW spr round 3 (radius: 5)
[27:59:54 -206656.879464] SLOW spr round 4 (radius: 10)
[28:01:59 -206656.879378] SLOW spr round 5 (radius: 15)
[28:04:59 -206654.397892] SLOW spr round 6 (radius: 5)
[28:07:34 -206654.397649] SLOW spr round 7 (radius: 10)
[28:09:59 -206654.397602] SLOW spr round 8 (radius: 15)
[28:12:44 -206654.397559] SLOW spr round 9 (radius: 20)
[28:17:04 -206651.982331] SLOW spr round 10 (radius: 5)
[28:19:41 -206649.499044] SLOW spr round 11 (radius: 5)
[28:22:01 -206649.498717] SLOW spr round 12 (radius: 10)
[28:24:13 -206649.498693] SLOW spr round 13 (radius: 15)
[28:27:00 -206649.498672] SLOW spr round 14 (radius: 20)
[28:31:16 -206649.498653] SLOW spr round 15 (radius: 25)
[28:36:49 -206649.498636] Model parameter optimization (eps = 0.100000)

[28:37:02] ML tree search #5, logLikelihood: -206649.290416

[28:37:02 -1066766.100253] Initial branch length optimization
[28:37:07 -876692.102779] Model parameter optimization (eps = 10.000000)
[28:37:49 -872894.947984] AUTODETECT spr round 1 (radius: 5)
[28:39:53 -496570.107309] AUTODETECT spr round 2 (radius: 10)
[28:42:04 -362321.769867] AUTODETECT spr round 3 (radius: 15)
[28:44:23 -282538.663917] AUTODETECT spr round 4 (radius: 20)
[28:46:52 -247330.971291] AUTODETECT spr round 5 (radius: 25)
[28:49:41 -237876.539604] SPR radius for FAST iterations: 25 (autodetect)
[28:49:41 -237876.539604] Model parameter optimization (eps = 3.000000)
[28:50:07 -237749.165951] FAST spr round 1 (radius: 25)
[28:52:33 -207817.793833] FAST spr round 2 (radius: 25)
[28:54:37 -206762.471875] FAST spr round 3 (radius: 25)
[28:56:28 -206716.964080] FAST spr round 4 (radius: 25)
[28:58:11 -206709.860222] FAST spr round 5 (radius: 25)
[28:59:48 -206709.858960] Model parameter optimization (eps = 1.000000)
[29:00:09 -206703.158628] SLOW spr round 1 (radius: 5)
[29:02:15 -206654.647865] SLOW spr round 2 (radius: 5)
[29:04:21 -206648.218211] SLOW spr round 3 (radius: 5)
[29:06:23 -206645.132120] SLOW spr round 4 (radius: 5)
[29:08:23 -206641.065810] SLOW spr round 5 (radius: 5)
[29:10:24 -206641.065802] SLOW spr round 6 (radius: 10)
[29:12:25 -206641.065796] SLOW spr round 7 (radius: 15)
[29:15:21 -206641.065791] SLOW spr round 8 (radius: 20)
[29:19:33 -206641.065785] SLOW spr round 9 (radius: 25)
[29:25:15 -206641.065779] Model parameter optimization (eps = 0.100000)

[29:25:26] ML tree search #6, logLikelihood: -206640.924691

[29:25:26 -1068209.638946] Initial branch length optimization
[29:25:31 -881932.123748] Model parameter optimization (eps = 10.000000)
[29:26:02 -877942.720263] AUTODETECT spr round 1 (radius: 5)
[29:28:07 -498118.092277] AUTODETECT spr round 2 (radius: 10)
[29:30:20 -357561.042191] AUTODETECT spr round 3 (radius: 15)
[29:32:36 -307112.848722] AUTODETECT spr round 4 (radius: 20)
[29:35:19 -256453.970542] AUTODETECT spr round 5 (radius: 25)
[29:37:56 -249784.067116] SPR radius for FAST iterations: 25 (autodetect)
[29:37:56 -249784.067116] Model parameter optimization (eps = 3.000000)
[29:38:17 -249625.872294] FAST spr round 1 (radius: 25)
[29:40:40 -212691.462387] FAST spr round 2 (radius: 25)
[29:42:45 -206957.724293] FAST spr round 3 (radius: 25)
[29:44:39 -206720.525802] FAST spr round 4 (radius: 25)
[29:46:23 -206720.509079] Model parameter optimization (eps = 1.000000)
[29:46:40 -206699.485871] SLOW spr round 1 (radius: 5)
[29:48:55 -206667.421987] SLOW spr round 2 (radius: 5)
[29:51:04 -206662.145115] SLOW spr round 3 (radius: 5)
[29:53:09 -206662.145071] SLOW spr round 4 (radius: 10)
[29:55:14 -206662.145065] SLOW spr round 5 (radius: 15)
[29:58:10 -206662.076595] SLOW spr round 6 (radius: 20)
[30:02:23 -206662.076422] SLOW spr round 7 (radius: 25)
[30:07:50 -206662.076419] Model parameter optimization (eps = 0.100000)

[30:07:56] ML tree search #7, logLikelihood: -206662.005323

[30:07:56 -1070478.750148] Initial branch length optimization
[30:08:01 -883422.526495] Model parameter optimization (eps = 10.000000)
[30:08:31 -879804.275791] AUTODETECT spr round 1 (radius: 5)
[30:10:33 -518318.382486] AUTODETECT spr round 2 (radius: 10)
[30:12:43 -359418.763324] AUTODETECT spr round 3 (radius: 15)
[30:15:05 -268392.510382] AUTODETECT spr round 4 (radius: 20)
[30:17:31 -240325.755177] AUTODETECT spr round 5 (radius: 25)
[30:20:07 -235601.670431] SPR radius for FAST iterations: 25 (autodetect)
[30:20:07 -235601.670431] Model parameter optimization (eps = 3.000000)
[30:20:30 -235421.348844] FAST spr round 1 (radius: 25)
[30:22:52 -208492.020655] FAST spr round 2 (radius: 25)
[30:24:51 -206875.288598] FAST spr round 3 (radius: 25)
[30:26:39 -206729.263462] FAST spr round 4 (radius: 25)
[30:28:17 -206729.262562] Model parameter optimization (eps = 1.000000)
[30:28:31 -206727.250286] SLOW spr round 1 (radius: 5)
[30:30:40 -206672.348386] SLOW spr round 2 (radius: 5)
[30:32:44 -206663.699411] SLOW spr round 3 (radius: 5)
[30:34:46 -206659.957961] SLOW spr round 4 (radius: 5)
[30:36:45 -206659.957869] SLOW spr round 5 (radius: 10)
[30:38:45 -206658.280452] SLOW spr round 6 (radius: 5)
[30:41:09 -206656.737760] SLOW spr round 7 (radius: 5)
[30:43:20 -206656.737702] SLOW spr round 8 (radius: 10)
[30:45:25 -206656.737669] SLOW spr round 9 (radius: 15)
[30:48:14 -206656.737642] SLOW spr round 10 (radius: 20)
[30:52:33 -206656.737618] SLOW spr round 11 (radius: 25)
[30:58:10 -206656.737597] Model parameter optimization (eps = 0.100000)

[30:58:19] ML tree search #8, logLikelihood: -206656.624810

[30:58:19 -1069422.079919] Initial branch length optimization
[30:58:24 -881307.771207] Model parameter optimization (eps = 10.000000)
[30:58:56 -877821.139691] AUTODETECT spr round 1 (radius: 5)
[31:00:57 -514296.821295] AUTODETECT spr round 2 (radius: 10)
[31:03:07 -371943.754573] AUTODETECT spr round 3 (radius: 15)
[31:05:31 -312123.724179] AUTODETECT spr round 4 (radius: 20)
[31:07:54 -283623.207830] AUTODETECT spr round 5 (radius: 25)
[31:10:32 -269997.309098] SPR radius for FAST iterations: 25 (autodetect)
[31:10:32 -269997.309098] Model parameter optimization (eps = 3.000000)
[31:10:51 -269849.071609] FAST spr round 1 (radius: 25)
[31:13:32 -210656.364131] FAST spr round 2 (radius: 25)
[31:15:42 -206940.079110] FAST spr round 3 (radius: 25)
[31:17:33 -206726.064052] FAST spr round 4 (radius: 25)
[31:19:14 -206712.277587] FAST spr round 5 (radius: 25)
[31:20:53 -206712.276949] Model parameter optimization (eps = 1.000000)
[31:21:09 -206705.438058] SLOW spr round 1 (radius: 5)
[31:23:20 -206655.312986] SLOW spr round 2 (radius: 5)
[31:25:28 -206649.875260] SLOW spr round 3 (radius: 5)
[31:27:31 -206649.438712] SLOW spr round 4 (radius: 5)
[31:29:35 -206649.438016] SLOW spr round 5 (radius: 10)
[31:31:40 -206649.255258] SLOW spr round 6 (radius: 5)
[31:34:11 -206647.713652] SLOW spr round 7 (radius: 5)
[31:36:27 -206647.713584] SLOW spr round 8 (radius: 10)
[31:38:35 -206647.713543] SLOW spr round 9 (radius: 15)
[31:41:27 -206647.490197] SLOW spr round 10 (radius: 5)
[31:44:04 -206645.386872] SLOW spr round 11 (radius: 5)
[31:46:22 -206645.386274] SLOW spr round 12 (radius: 10)
[31:48:34 -206645.386265] SLOW spr round 13 (radius: 15)
[31:51:23 -206645.386257] SLOW spr round 14 (radius: 20)
[31:55:43 -206645.386249] SLOW spr round 15 (radius: 25)
[32:01:25 -206645.386242] Model parameter optimization (eps = 0.100000)

[32:01:33] ML tree search #9, logLikelihood: -206645.222450

[32:01:33 -1075846.420369] Initial branch length optimization
[32:01:39 -886536.439323] Model parameter optimization (eps = 10.000000)
[32:02:19 -882666.873466] AUTODETECT spr round 1 (radius: 5)
[32:04:19 -522403.270986] AUTODETECT spr round 2 (radius: 10)
[32:06:28 -364807.316604] AUTODETECT spr round 3 (radius: 15)
[32:08:46 -302355.576951] AUTODETECT spr round 4 (radius: 20)
[32:11:10 -254841.687614] AUTODETECT spr round 5 (radius: 25)
[32:13:48 -243017.903499] SPR radius for FAST iterations: 25 (autodetect)
[32:13:48 -243017.903499] Model parameter optimization (eps = 3.000000)
[32:14:11 -242813.411331] FAST spr round 1 (radius: 25)
[32:16:37 -208313.528651] FAST spr round 2 (radius: 25)
[32:18:35 -206800.325358] FAST spr round 3 (radius: 25)
[32:20:20 -206747.708958] FAST spr round 4 (radius: 25)
[32:22:01 -206742.711154] FAST spr round 5 (radius: 25)
[32:23:36 -206742.710928] Model parameter optimization (eps = 1.000000)
[32:23:51 -206735.050387] SLOW spr round 1 (radius: 5)
[32:26:01 -206678.336867] SLOW spr round 2 (radius: 5)
[32:28:09 -206673.024429] SLOW spr round 3 (radius: 5)
[32:30:15 -206668.656821] SLOW spr round 4 (radius: 5)
[32:32:19 -206668.656660] SLOW spr round 5 (radius: 10)
[32:34:22 -206667.382154] SLOW spr round 6 (radius: 5)
[32:36:50 -206667.222451] SLOW spr round 7 (radius: 5)
[32:39:05 -206667.222305] SLOW spr round 8 (radius: 10)
[32:41:14 -206667.222251] SLOW spr round 9 (radius: 15)
[32:44:01 -206667.150092] SLOW spr round 10 (radius: 20)
[32:48:17 -206667.149886] SLOW spr round 11 (radius: 25)
[32:53:50 -206667.149851] Model parameter optimization (eps = 0.100000)

[32:54:06] ML tree search #10, logLikelihood: -206666.718848

[32:54:06 -1069551.428704] Initial branch length optimization
[32:54:11 -885366.627889] Model parameter optimization (eps = 10.000000)
[32:54:46 -881972.894688] AUTODETECT spr round 1 (radius: 5)
[32:56:53 -507107.394727] AUTODETECT spr round 2 (radius: 10)
[32:59:05 -370755.798993] AUTODETECT spr round 3 (radius: 15)
[33:01:30 -302772.329537] AUTODETECT spr round 4 (radius: 20)
[33:03:57 -257019.090790] AUTODETECT spr round 5 (radius: 25)
[33:06:32 -245303.536768] SPR radius for FAST iterations: 25 (autodetect)
[33:06:32 -245303.536768] Model parameter optimization (eps = 3.000000)
[33:06:43 -245295.749026] FAST spr round 1 (radius: 25)
[33:09:09 -208624.534630] FAST spr round 2 (radius: 25)
[33:11:09 -207038.361286] FAST spr round 3 (radius: 25)
[33:12:58 -206871.538353] FAST spr round 4 (radius: 25)
[33:14:42 -206858.613340] FAST spr round 5 (radius: 25)
[33:16:19 -206855.246556] FAST spr round 6 (radius: 25)
[33:17:57 -206855.246422] Model parameter optimization (eps = 1.000000)
[33:18:15 -206696.323063] SLOW spr round 1 (radius: 5)
[33:20:23 -206664.491967] SLOW spr round 2 (radius: 5)
[33:22:30 -206649.469153] SLOW spr round 3 (radius: 5)
[33:24:36 -206649.463060] SLOW spr round 4 (radius: 10)
[33:26:40 -206649.463026] SLOW spr round 5 (radius: 15)
[33:29:34 -206649.463003] SLOW spr round 6 (radius: 20)
[33:33:39 -206649.462983] SLOW spr round 7 (radius: 25)
[33:39:08 -206649.462966] Model parameter optimization (eps = 0.100000)

[33:39:18] ML tree search #11, logLikelihood: -206649.313679

[33:39:18 -1078254.236947] Initial branch length optimization
[33:39:26 -886657.858410] Model parameter optimization (eps = 10.000000)
[33:39:56 -883128.442127] AUTODETECT spr round 1 (radius: 5)
[33:41:55 -518322.051946] AUTODETECT spr round 2 (radius: 10)
[33:44:03 -370470.925734] AUTODETECT spr round 3 (radius: 15)
[33:46:28 -296910.463082] AUTODETECT spr round 4 (radius: 20)
[33:48:53 -258060.364647] AUTODETECT spr round 5 (radius: 25)
[33:51:43 -248342.012920] SPR radius for FAST iterations: 25 (autodetect)
[33:51:43 -248342.012920] Model parameter optimization (eps = 3.000000)
[33:52:00 -248167.452137] FAST spr round 1 (radius: 25)
[33:54:20 -212408.920522] FAST spr round 2 (radius: 25)
[33:56:17 -207408.195105] FAST spr round 3 (radius: 25)
[33:58:07 -206753.352262] FAST spr round 4 (radius: 25)
[33:59:51 -206737.631114] FAST spr round 5 (radius: 25)
[34:01:29 -206737.630647] Model parameter optimization (eps = 1.000000)
[34:01:46 -206726.402308] SLOW spr round 1 (radius: 5)
[34:03:55 -206685.318772] SLOW spr round 2 (radius: 5)
[34:06:01 -206680.702088] SLOW spr round 3 (radius: 5)
[34:08:04 -206679.982631] SLOW spr round 4 (radius: 5)
[34:10:05 -206679.936975] SLOW spr round 5 (radius: 10)
[34:12:06 -206677.970356] SLOW spr round 6 (radius: 5)
[34:14:31 -206677.970149] SLOW spr round 7 (radius: 10)
[34:16:48 -206677.970083] SLOW spr round 8 (radius: 15)
[34:19:34 -206677.970025] SLOW spr round 9 (radius: 20)
[34:23:48 -206677.969971] SLOW spr round 10 (radius: 25)
[34:29:18 -206677.969923] Model parameter optimization (eps = 0.100000)

[34:29:27] ML tree search #12, logLikelihood: -206677.806537

[34:29:27 -1075175.843195] Initial branch length optimization
[34:29:32 -886535.872437] Model parameter optimization (eps = 10.000000)
[34:30:00 -882603.590212] AUTODETECT spr round 1 (radius: 5)
[34:32:05 -501709.413609] AUTODETECT spr round 2 (radius: 10)
[34:34:16 -360989.781391] AUTODETECT spr round 3 (radius: 15)
[34:36:38 -304606.955527] AUTODETECT spr round 4 (radius: 20)
[34:39:21 -276680.919408] AUTODETECT spr round 5 (radius: 25)
[34:42:21 -252110.962417] SPR radius for FAST iterations: 25 (autodetect)
[34:42:21 -252110.962417] Model parameter optimization (eps = 3.000000)
[34:42:38 -251951.083255] FAST spr round 1 (radius: 25)
[34:45:07 -209008.833095] FAST spr round 2 (radius: 25)
[34:47:07 -206931.487691] FAST spr round 3 (radius: 25)
[34:48:58 -206800.691720] FAST spr round 4 (radius: 25)
[34:50:42 -206734.544637] FAST spr round 5 (radius: 25)
[34:52:24 -206725.780979] FAST spr round 6 (radius: 25)
[34:54:02 -206725.294678] FAST spr round 7 (radius: 25)
[34:55:37 -206725.294097] Model parameter optimization (eps = 1.000000)
[34:55:53 -206714.100005] SLOW spr round 1 (radius: 5)
[34:57:59 -206671.489730] SLOW spr round 2 (radius: 5)
[35:00:05 -206666.728335] SLOW spr round 3 (radius: 5)
[35:02:08 -206659.791122] SLOW spr round 4 (radius: 5)
[35:04:17 -206659.791101] SLOW spr round 5 (radius: 10)
[35:06:19 -206658.293225] SLOW spr round 6 (radius: 5)
[35:08:44 -206653.743210] SLOW spr round 7 (radius: 5)
[35:10:57 -206653.742997] SLOW spr round 8 (radius: 10)
[35:13:03 -206653.742989] SLOW spr round 9 (radius: 15)
[35:15:50 -206653.677056] SLOW spr round 10 (radius: 20)
[35:19:59 -206653.676875] SLOW spr round 11 (radius: 25)
[35:25:29 -206653.676866] Model parameter optimization (eps = 0.100000)

[35:25:40] ML tree search #13, logLikelihood: -206653.493102

[35:25:40 -1074083.364131] Initial branch length optimization
[35:25:45 -885783.821759] Model parameter optimization (eps = 10.000000)
[35:26:14 -882140.889217] AUTODETECT spr round 1 (radius: 5)
[35:28:21 -510004.648410] AUTODETECT spr round 2 (radius: 10)
[35:30:36 -370014.195220] AUTODETECT spr round 3 (radius: 15)
[35:33:05 -304202.738917] AUTODETECT spr round 4 (radius: 20)
[35:35:41 -263254.840940] AUTODETECT spr round 5 (radius: 25)
[35:38:35 -247177.199091] SPR radius for FAST iterations: 25 (autodetect)
[35:38:35 -247177.199091] Model parameter optimization (eps = 3.000000)
[35:38:55 -247047.251296] FAST spr round 1 (radius: 25)
[35:41:19 -208589.863437] FAST spr round 2 (radius: 25)
[35:43:16 -206823.753398] FAST spr round 3 (radius: 25)
[35:45:07 -206700.401917] FAST spr round 4 (radius: 25)
[35:46:50 -206692.567592] FAST spr round 5 (radius: 25)
[35:48:30 -206690.790776] FAST spr round 6 (radius: 25)
[35:50:08 -206690.790650] Model parameter optimization (eps = 1.000000)
[35:50:25 -206676.571237] SLOW spr round 1 (radius: 5)
[35:52:35 -206645.686491] SLOW spr round 2 (radius: 5)
[35:54:43 -206644.900227] SLOW spr round 3 (radius: 5)
[35:56:49 -206644.899882] SLOW spr round 4 (radius: 10)
[35:58:53 -206644.124229] SLOW spr round 5 (radius: 5)
[36:01:20 -206644.124220] SLOW spr round 6 (radius: 10)
[36:03:40 -206644.124218] SLOW spr round 7 (radius: 15)
[36:06:27 -206644.124216] SLOW spr round 8 (radius: 20)
[36:10:53 -206644.124215] SLOW spr round 9 (radius: 25)
[36:16:28 -206644.124214] Model parameter optimization (eps = 0.100000)

[36:16:40] ML tree search #14, logLikelihood: -206643.915060

[36:16:40 -1080779.307703] Initial branch length optimization
[36:16:46 -892387.075913] Model parameter optimization (eps = 10.000000)
[36:17:21 -888655.403490] AUTODETECT spr round 1 (radius: 5)
[36:19:26 -503206.375237] AUTODETECT spr round 2 (radius: 10)
[36:21:39 -364444.640880] AUTODETECT spr round 3 (radius: 15)
[36:24:03 -287125.800477] AUTODETECT spr round 4 (radius: 20)
[36:26:27 -251521.912566] AUTODETECT spr round 5 (radius: 25)
[36:29:06 -242481.113282] SPR radius for FAST iterations: 25 (autodetect)
[36:29:06 -242481.113282] Model parameter optimization (eps = 3.000000)
[36:29:28 -242310.902885] FAST spr round 1 (radius: 25)
[36:31:52 -208155.851847] FAST spr round 2 (radius: 25)
[36:33:50 -206814.080469] FAST spr round 3 (radius: 25)
[36:35:39 -206719.613598] FAST spr round 4 (radius: 25)
[36:37:20 -206713.536684] FAST spr round 5 (radius: 25)
[36:38:57 -206713.519547] Model parameter optimization (eps = 1.000000)
[36:39:09 -206709.537075] SLOW spr round 1 (radius: 5)
[36:41:16 -206674.116782] SLOW spr round 2 (radius: 5)
[36:43:19 -206662.437709] SLOW spr round 3 (radius: 5)
[36:45:19 -206662.437429] SLOW spr round 4 (radius: 10)
[36:47:22 -206662.437287] SLOW spr round 5 (radius: 15)
[36:50:19 -206662.437176] SLOW spr round 6 (radius: 20)
[36:54:36 -206662.437079] SLOW spr round 7 (radius: 25)
[37:00:23 -206662.436993] Model parameter optimization (eps = 0.100000)

[37:00:31] ML tree search #15, logLikelihood: -206662.362287

[37:00:31 -1074510.340172] Initial branch length optimization
[37:00:36 -882338.027600] Model parameter optimization (eps = 10.000000)
[37:01:25 -878749.505150] AUTODETECT spr round 1 (radius: 5)
[37:03:29 -505633.840721] AUTODETECT spr round 2 (radius: 10)
[37:05:38 -353573.965668] AUTODETECT spr round 3 (radius: 15)
[37:07:56 -283672.443654] AUTODETECT spr round 4 (radius: 20)
[37:10:27 -248274.973337] AUTODETECT spr round 5 (radius: 25)
[37:13:16 -239193.695607] SPR radius for FAST iterations: 25 (autodetect)
[37:13:16 -239193.695607] Model parameter optimization (eps = 3.000000)
[37:13:34 -239000.137739] FAST spr round 1 (radius: 25)
[37:16:03 -208336.428252] FAST spr round 2 (radius: 25)
[37:18:10 -206785.455408] FAST spr round 3 (radius: 25)
[37:20:08 -206699.316442] FAST spr round 4 (radius: 25)
[37:21:49 -206693.071118] FAST spr round 5 (radius: 25)
[37:23:27 -206693.069136] Model parameter optimization (eps = 1.000000)
[37:23:41 -206692.038856] SLOW spr round 1 (radius: 5)
[37:25:50 -206659.181749] SLOW spr round 2 (radius: 5)
[37:27:55 -206652.797623] SLOW spr round 3 (radius: 5)
[37:29:54 -206652.797164] SLOW spr round 4 (radius: 10)
[37:31:57 -206652.797047] SLOW spr round 5 (radius: 15)
[37:34:52 -206652.728900] SLOW spr round 6 (radius: 20)
[37:39:06 -206652.728707] SLOW spr round 7 (radius: 25)
[37:44:46 -206652.728688] Model parameter optimization (eps = 0.100000)

[37:44:58] ML tree search #16, logLikelihood: -206652.575150

[37:44:58 -1067750.556159] Initial branch length optimization
[37:45:03 -881992.199147] Model parameter optimization (eps = 10.000000)
[37:45:37 -878332.425754] AUTODETECT spr round 1 (radius: 5)
[37:47:40 -509096.749695] AUTODETECT spr round 2 (radius: 10)
[37:49:48 -355325.186596] AUTODETECT spr round 3 (radius: 15)
[37:52:13 -296915.421795] AUTODETECT spr round 4 (radius: 20)
[37:54:40 -272640.257627] AUTODETECT spr round 5 (radius: 25)
[37:57:25 -262883.245217] SPR radius for FAST iterations: 25 (autodetect)
[37:57:25 -262883.245217] Model parameter optimization (eps = 3.000000)
[37:57:44 -262739.195930] FAST spr round 1 (radius: 25)
[38:00:10 -211563.973686] FAST spr round 2 (radius: 25)
[38:02:06 -207247.307415] FAST spr round 3 (radius: 25)
[38:03:55 -206739.877412] FAST spr round 4 (radius: 25)
[38:05:37 -206724.385643] FAST spr round 5 (radius: 25)
[38:07:13 -206717.069047] FAST spr round 6 (radius: 25)
[38:08:49 -206715.898913] FAST spr round 7 (radius: 25)
[38:10:22 -206715.898861] Model parameter optimization (eps = 1.000000)
[38:10:37 -206712.318316] SLOW spr round 1 (radius: 5)
[38:12:41 -206654.156001] SLOW spr round 2 (radius: 5)
[38:14:44 -206654.154518] SLOW spr round 3 (radius: 10)
[38:16:46 -206654.154359] SLOW spr round 4 (radius: 15)
[38:19:59 -206654.154324] SLOW spr round 5 (radius: 20)
[38:24:10 -206654.154313] SLOW spr round 6 (radius: 25)
[38:29:40 -206654.154308] Model parameter optimization (eps = 0.100000)

[38:29:50] ML tree search #17, logLikelihood: -206653.982776

[38:29:50 -1060259.474858] Initial branch length optimization
[38:29:57 -868293.815659] Model parameter optimization (eps = 10.000000)
[38:30:24 -865005.535849] AUTODETECT spr round 1 (radius: 5)
[38:32:23 -516358.633199] AUTODETECT spr round 2 (radius: 10)
[38:34:30 -348232.201091] AUTODETECT spr round 3 (radius: 15)
[38:36:42 -290599.075380] AUTODETECT spr round 4 (radius: 20)
[38:39:18 -244991.980605] AUTODETECT spr round 5 (radius: 25)
[38:42:25 -242555.322258] SPR radius for FAST iterations: 25 (autodetect)
[38:42:25 -242555.322258] Model parameter optimization (eps = 3.000000)
[38:42:45 -242435.483453] FAST spr round 1 (radius: 25)
[38:45:14 -207941.837651] FAST spr round 2 (radius: 25)
[38:47:13 -206789.345932] FAST spr round 3 (radius: 25)
[38:48:59 -206736.728238] FAST spr round 4 (radius: 25)
[38:50:36 -206727.896208] FAST spr round 5 (radius: 25)
[38:52:10 -206727.896010] Model parameter optimization (eps = 1.000000)
[38:52:24 -206726.438766] SLOW spr round 1 (radius: 5)
[38:54:35 -206686.327119] SLOW spr round 2 (radius: 5)
[38:56:38 -206680.103363] SLOW spr round 3 (radius: 5)
[38:58:38 -206676.033933] SLOW spr round 4 (radius: 5)
[39:00:36 -206676.033598] SLOW spr round 5 (radius: 10)
[39:02:35 -206675.257616] SLOW spr round 6 (radius: 5)
[39:05:02 -206675.257570] SLOW spr round 7 (radius: 10)
[39:07:24 -206675.257545] SLOW spr round 8 (radius: 15)
[39:10:15 -206674.765921] SLOW spr round 9 (radius: 5)
[39:12:51 -206674.765867] SLOW spr round 10 (radius: 10)
[39:15:18 -206674.765854] SLOW spr round 11 (radius: 15)
[39:18:06 -206674.765844] SLOW spr round 12 (radius: 20)
[39:22:37 -206674.765834] SLOW spr round 13 (radius: 25)
[39:28:16 -206674.765826] Model parameter optimization (eps = 0.100000)

[39:28:28] ML tree search #18, logLikelihood: -206674.378496

[39:28:28 -1070863.821857] Initial branch length optimization
[39:28:34 -883664.989230] Model parameter optimization (eps = 10.000000)
[39:29:17 -880061.394850] AUTODETECT spr round 1 (radius: 5)
[40:43:44 -502529.105943] AUTODETECT spr round 2 (radius: 10)
[41:57:35 -355803.275982] AUTODETECT spr round 3 (radius: 15)
[42:48:29 -283406.441425] AUTODETECT spr round 4 (radius: 20)
[43:36:16 -249832.771282] AUTODETECT spr round 5 (radius: 25)
[43:59:15 -242169.234818] SPR radius for FAST iterations: 25 (autodetect)
[43:59:15 -242169.234818] Model parameter optimization (eps = 3.000000)
[43:59:34 -242008.170544] FAST spr round 1 (radius: 25)
[44:35:22 -208079.044860] FAST spr round 2 (radius: 25)
[44:49:03 -206811.371040] FAST spr round 3 (radius: 25)
[45:03:49 -206730.602836] FAST spr round 4 (radius: 25)
[45:06:09 -206722.521908] FAST spr round 5 (radius: 25)
[45:08:38 -206722.521426] Model parameter optimization (eps = 1.000000)
[45:08:53 -206720.637264] SLOW spr round 1 (radius: 5)
[45:12:16 -206673.543252] SLOW spr round 2 (radius: 5)
[45:15:29 -206665.649552] SLOW spr round 3 (radius: 5)
[45:18:18 -206665.648967] SLOW spr round 4 (radius: 10)
[45:21:25 -206664.182576] SLOW spr round 5 (radius: 5)
[45:24:52 -206658.121056] SLOW spr round 6 (radius: 5)
[45:28:36 -206658.120805] SLOW spr round 7 (radius: 10)
[45:31:21 -206658.120797] SLOW spr round 8 (radius: 15)
[45:35:44 -206658.120793] SLOW spr round 9 (radius: 20)
[46:02:49 -206658.060175] SLOW spr round 10 (radius: 25)
[46:12:34 -206658.060001] Model parameter optimization (eps = 0.100000)

[46:12:47] ML tree search #19, logLikelihood: -206657.762640

[46:12:48 -1075241.914582] Initial branch length optimization
[46:12:53 -888184.152791] Model parameter optimization (eps = 10.000000)
[46:13:29 -884275.207279] AUTODETECT spr round 1 (radius: 5)
[46:17:51 -508043.541799] AUTODETECT spr round 2 (radius: 10)
[46:21:24 -363603.837431] AUTODETECT spr round 3 (radius: 15)
[46:25:01 -289788.160164] AUTODETECT spr round 4 (radius: 20)
[46:29:05 -263317.264124] AUTODETECT spr round 5 (radius: 25)
[46:33:31 -243822.851261] SPR radius for FAST iterations: 25 (autodetect)
[46:33:31 -243822.851261] Model parameter optimization (eps = 3.000000)
[46:33:52 -243644.251736] FAST spr round 1 (radius: 25)
[46:38:36 -208804.677675] FAST spr round 2 (radius: 25)
[46:41:40 -206785.710444] FAST spr round 3 (radius: 25)
[46:44:17 -206726.979403] FAST spr round 4 (radius: 25)
[46:46:48 -206725.337243] FAST spr round 5 (radius: 25)
[46:49:13 -206725.336977] Model parameter optimization (eps = 1.000000)
[46:49:28 -206716.398698] SLOW spr round 1 (radius: 5)
[46:52:30 -206679.272040] SLOW spr round 2 (radius: 5)
[46:55:53 -206667.732967] SLOW spr round 3 (radius: 5)
[46:59:00 -206666.934256] SLOW spr round 4 (radius: 5)
[47:01:53 -206666.934213] SLOW spr round 5 (radius: 10)
[47:04:58 -206665.336767] SLOW spr round 6 (radius: 5)
[47:08:58 -206665.336693] SLOW spr round 7 (radius: 10)
[47:12:37 -206665.336686] SLOW spr round 8 (radius: 15)
[47:16:51 -206665.336680] SLOW spr round 9 (radius: 20)
[47:23:34 -206665.336675] SLOW spr round 10 (radius: 25)
[47:32:38 -206665.336670] Model parameter optimization (eps = 0.100000)

[47:32:48] ML tree search #20, logLikelihood: -206665.064626


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.231804,0.525552) (0.205861,0.546810) (0.375808,0.944856) (0.186527,2.200877) 
   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: -206640.924691

AIC score: 417291.849382 / AICc score: 8461351.849382 / BIC score: 426147.397609
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=612).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9HCR9/3_mltree/Q9HCR9.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9HCR9/3_mltree/Q9HCR9.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9HCR9/3_mltree/Q9HCR9.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q9HCR9/3_mltree/Q9HCR9.raxml.log

Analysis started: 04-Jul-2021 02:23:22 / finished: 06-Jul-2021 01:56:11

Elapsed time: 171169.107 seconds