RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

System: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM

RAxML-NG was called at 03-Jul-2021 00:06:39 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UHX3/2_msa/Q9UHX3_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UHX3/3_mltree/Q9UHX3 --seed 2 --threads 7 --tree rand{20} pars{20}

Analysis options:
  run mode: ML tree search
  start tree(s): random (20)
  random seed: 2
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (7 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UHX3/2_msa/Q9UHX3_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 580 sites

WARNING: Sequences sp_Q80TR1_AGRL1_MOUSE_10090 and tr_A0A1U8D2E1_A0A1U8D2E1_MESAU_10036 are exactly identical!
WARNING: Sequences sp_Q80TS3_AGRL3_MOUSE_10090 and tr_F7ACL7_F7ACL7_HORSE_9796 are exactly identical!
WARNING: Sequences sp_Q80TS3_AGRL3_MOUSE_10090 and tr_A0A1U8BJX5_A0A1U8BJX5_MESAU_10036 are exactly identical!
WARNING: Sequences tr_A0A2I2Y2R6_A0A2I2Y2R6_GORGO_9595 and sp_O94910_AGRL1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2Y2R6_A0A2I2Y2R6_GORGO_9595 and tr_F7C0V2_F7C0V2_MACMU_9544 are exactly identical!
WARNING: Sequences tr_A0A2I2Y2R6_A0A2I2Y2R6_GORGO_9595 and tr_U3FRU9_U3FRU9_CALJA_9483 are exactly identical!
WARNING: Sequences tr_A0A2I2Y2R6_A0A2I2Y2R6_GORGO_9595 and tr_A0A0A0MU59_A0A0A0MU59_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A2I2Y2R6_A0A2I2Y2R6_GORGO_9595 and tr_A0A0D9R202_A0A0D9R202_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I2Y2R6_A0A2I2Y2R6_GORGO_9595 and tr_A0A2K5NNE1_A0A2K5NNE1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I2Y2R6_A0A2I2Y2R6_GORGO_9595 and tr_A0A2K6AUX8_A0A2K6AUX8_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A2I2Y2R6_A0A2I2Y2R6_GORGO_9595 and tr_A0A2K6A057_A0A2K6A057_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I2Y2R6_A0A2I2Y2R6_GORGO_9595 and tr_A0A2R8ZME8_A0A2R8ZME8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I2Y9M5_A0A2I2Y9M5_GORGO_9595 and tr_A0A2I3SPU9_A0A2I3SPU9_PANTR_9598 are exactly identical!
WARNING: Sequences tr_E2R3S4_E2R3S4_CANLF_9615 and tr_G5BYT1_G5BYT1_HETGA_10181 are exactly identical!
WARNING: Sequences tr_E2R3S4_E2R3S4_CANLF_9615 and tr_G1M3S9_G1M3S9_AILME_9646 are exactly identical!
WARNING: Sequences tr_E2R3S4_E2R3S4_CANLF_9615 and tr_L5K5D5_L5K5D5_PTEAL_9402 are exactly identical!
WARNING: Sequences tr_E2R3S4_E2R3S4_CANLF_9615 and tr_A0A2Y9LYP0_A0A2Y9LYP0_DELLE_9749 are exactly identical!
WARNING: Sequences tr_E2R3S4_E2R3S4_CANLF_9615 and tr_A0A2Y9TID1_A0A2Y9TID1_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_F1PJ45_F1PJ45_CANLF_9615 and tr_A0A384B1U6_A0A384B1U6_BALAS_310752 are exactly identical!
WARNING: Sequences tr_A0A2I3RYF0_A0A2I3RYF0_PANTR_9598 and tr_F7IMA1_F7IMA1_CALJA_9483 are exactly identical!
WARNING: Sequences tr_A0A2I3RYF0_A0A2I3RYF0_PANTR_9598 and tr_A0A2R8ZYR9_A0A2R8ZYR9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3TB47_A0A2I3TB47_PANTR_9598 and tr_A0A2R9A621_A0A2R9A621_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2J8JP78_A0A2J8JP78_PANTR_9598 and sp_Q8IZF6_AGRG4_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2J8JP78_A0A2J8JP78_PANTR_9598 and tr_A0A2R9BYS8_A0A2R9BYS8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F7E9A3_F7E9A3_MONDO_13616 and tr_G3W2L4_G3W2L4_SARHA_9305 are exactly identical!
WARNING: Sequences tr_W5PVX9_W5PVX9_SHEEP_9940 and tr_F1MZ63_F1MZ63_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_W5PVX9_W5PVX9_SHEEP_9940 and sp_O97817_AGRL2_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A3B5RBQ4_A0A3B5RBQ4_XIPMA_8083 and tr_A0A087XHR7_A0A087XHR7_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A0A1D5Q5W8_A0A1D5Q5W8_MACMU_9544 and tr_A0A2I3LF52_A0A2I3LF52_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5Q5W8_A0A1D5Q5W8_MACMU_9544 and tr_A0A2K5KQB7_A0A2K5KQB7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7HED3_F7HED3_MACMU_9544 and tr_A0A2I3LRM3_A0A2I3LRM3_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7HED3_F7HED3_MACMU_9544 and tr_A0A2K5LJ33_A0A2K5LJ33_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7HED3_F7HED3_MACMU_9544 and tr_A0A2K6DDZ5_A0A2K6DDZ5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7HED3_F7HED3_MACMU_9544 and tr_A0A2K5YFR8_A0A2K5YFR8_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H0Z8M7_H0Z8M7_TAEGU_59729 and tr_A0A218VE44_A0A218VE44_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A0A151P2J9_A0A151P2J9_ALLMI_8496 and tr_A0A3Q0FQV3_A0A3Q0FQV3_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A091JGC1_A0A091JGC1_EGRGA_188379 and tr_A0A091VB51_A0A091VB51_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091JGC1_A0A091JGC1_EGRGA_188379 and tr_A0A087RHE7_A0A087RHE7_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A2I0ME39_A0A2I0ME39_COLLI_8932 and tr_A0A1V4JZ35_A0A1V4JZ35_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A0V0ZTY0_A0A0V0ZTY0_9BILA_990121 and tr_A0A0V1P4J1_A0A0V1P4J1_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V0ZTY0_A0A0V0ZTY0_9BILA_990121 and tr_A0A0V0U146_A0A0V0U146_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A226NH93_A0A226NH93_CALSU_9009 and tr_A0A226PIY7_A0A226PIY7_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0QEZ6_A0A2D0QEZ6_ICTPU_7998 and tr_A0A2D0QFZ6_A0A2D0QFZ6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QEZ6_A0A2D0QEZ6_ICTPU_7998 and tr_A0A2D0QHD6_A0A2D0QHD6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QEZ6_A0A2D0QEZ6_ICTPU_7998 and tr_A0A2D0QI94_A0A2D0QI94_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0RR99_A0A2D0RR99_ICTPU_7998 and tr_A0A2D0RS89_A0A2D0RS89_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0T4Z7_A0A2D0T4Z7_ICTPU_7998 and tr_A0A2D0T4Z8_A0A2D0T4Z8_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0T4Z7_A0A2D0T4Z7_ICTPU_7998 and tr_A0A2D0T509_A0A2D0T509_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0T4Z7_A0A2D0T4Z7_ICTPU_7998 and tr_A0A2D0T589_A0A2D0T589_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U3VJF2_A0A2U3VJF2_ODORO_9708 and tr_A0A2Y9MD40_A0A2Y9MD40_DELLE_9749 are exactly identical!
WARNING: Duplicate sequences found: 50

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UHX3/3_mltree/Q9UHX3.raxml.reduced.phy

Alignment comprises 1 partitions and 580 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 580 / 580
Gaps: 12.96 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UHX3/3_mltree/Q9UHX3.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 / 83 / 6640
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1005645.493739] Initial branch length optimization
[00:00:05 -817266.972116] Model parameter optimization (eps = 10.000000)
[00:01:07 -814800.267517] AUTODETECT spr round 1 (radius: 5)
[00:04:24 -605185.025482] AUTODETECT spr round 2 (radius: 10)
[00:06:29 -457621.658564] AUTODETECT spr round 3 (radius: 15)
[00:08:58 -370110.352453] AUTODETECT spr round 4 (radius: 20)
[00:11:47 -324363.144894] AUTODETECT spr round 5 (radius: 25)
[00:14:54 -318607.367455] SPR radius for FAST iterations: 25 (autodetect)
[00:14:54 -318607.367455] Model parameter optimization (eps = 3.000000)
[00:15:15 -318233.592368] FAST spr round 1 (radius: 25)
[00:17:43 -271225.063096] FAST spr round 2 (radius: 25)
[00:19:42 -269085.124009] FAST spr round 3 (radius: 25)
[00:21:23 -269014.976863] FAST spr round 4 (radius: 25)
[00:22:57 -269005.280376] FAST spr round 5 (radius: 25)
[00:24:29 -269003.914932] FAST spr round 6 (radius: 25)
[00:26:01 -269003.912485] Model parameter optimization (eps = 1.000000)
[00:26:14 -269001.534324] SLOW spr round 1 (radius: 5)
[00:28:13 -268939.953226] SLOW spr round 2 (radius: 5)
[00:30:10 -268930.160258] SLOW spr round 3 (radius: 5)
[00:32:06 -268926.493444] SLOW spr round 4 (radius: 5)
[00:33:58 -268925.913681] SLOW spr round 5 (radius: 5)
[00:35:49 -268925.913506] SLOW spr round 6 (radius: 10)
[00:37:48 -268925.420336] SLOW spr round 7 (radius: 5)
[00:40:09 -268925.419513] SLOW spr round 8 (radius: 10)
[00:42:15 -268925.419413] SLOW spr round 9 (radius: 15)
[00:45:06 -268925.419357] SLOW spr round 10 (radius: 20)
[00:50:09 -268925.419309] SLOW spr round 11 (radius: 25)
[00:56:47 -268388.102954] SLOW spr round 12 (radius: 5)
[00:59:22 -268182.242290] SLOW spr round 13 (radius: 5)
[01:01:37 -268178.940157] SLOW spr round 14 (radius: 5)
[01:03:38 -268166.256198] SLOW spr round 15 (radius: 5)
[01:05:32 -268166.255798] SLOW spr round 16 (radius: 10)
[01:07:29 -268166.255745] SLOW spr round 17 (radius: 15)
[01:10:24 -268166.255719] SLOW spr round 18 (radius: 20)
[01:15:27 -268166.255696] SLOW spr round 19 (radius: 25)
[01:22:15 -268166.255674] Model parameter optimization (eps = 0.100000)

[01:22:23] ML tree search #1, logLikelihood: -268165.941147

[01:22:23 -1012928.613434] Initial branch length optimization
[01:22:28 -823161.771537] Model parameter optimization (eps = 10.000000)
[01:23:11 -820917.533288] AUTODETECT spr round 1 (radius: 5)
[01:25:08 -600584.337593] AUTODETECT spr round 2 (radius: 10)
[01:27:13 -444670.821113] AUTODETECT spr round 3 (radius: 15)
[01:29:31 -355017.616076] AUTODETECT spr round 4 (radius: 20)
[01:32:09 -318134.924063] AUTODETECT spr round 5 (radius: 25)
[01:35:29 -309796.989560] SPR radius for FAST iterations: 25 (autodetect)
[01:35:29 -309796.989560] Model parameter optimization (eps = 3.000000)
[01:35:53 -309331.431437] FAST spr round 1 (radius: 25)
[01:38:26 -269954.517192] FAST spr round 2 (radius: 25)
[01:40:26 -268432.956717] FAST spr round 3 (radius: 25)
[01:42:13 -268335.561196] FAST spr round 4 (radius: 25)
[01:43:51 -268313.449925] FAST spr round 5 (radius: 25)
[01:45:23 -268309.042032] FAST spr round 6 (radius: 25)
[01:46:51 -268309.041937] Model parameter optimization (eps = 1.000000)
[01:47:04 -268300.727814] SLOW spr round 1 (radius: 5)
[01:49:02 -268239.533592] SLOW spr round 2 (radius: 5)
[01:50:58 -268230.526428] SLOW spr round 3 (radius: 5)
[01:52:48 -268230.526215] SLOW spr round 4 (radius: 10)
[01:54:44 -268229.995355] SLOW spr round 5 (radius: 5)
[01:57:00 -268229.995315] SLOW spr round 6 (radius: 10)
[01:59:02 -268229.995292] SLOW spr round 7 (radius: 15)
[02:01:47 -268229.995273] SLOW spr round 8 (radius: 20)
[02:06:41 -268229.995254] SLOW spr round 9 (radius: 25)
[02:13:10 -268217.104901] SLOW spr round 10 (radius: 5)
[02:15:47 -268159.287818] SLOW spr round 11 (radius: 5)
[02:17:58 -268157.211375] SLOW spr round 12 (radius: 5)
[02:19:56 -268157.211115] SLOW spr round 13 (radius: 10)
[02:21:55 -268157.211087] SLOW spr round 14 (radius: 15)
[02:24:44 -268157.211066] SLOW spr round 15 (radius: 20)
[02:29:40 -268157.211047] SLOW spr round 16 (radius: 25)
[02:36:09 -268157.211028] Model parameter optimization (eps = 0.100000)

[02:36:13] ML tree search #2, logLikelihood: -268157.198823

[02:36:13 -1002636.217235] Initial branch length optimization
[02:36:17 -814143.706942] Model parameter optimization (eps = 10.000000)
[02:37:12 -811927.497667] AUTODETECT spr round 1 (radius: 5)
[02:39:09 -600771.726519] AUTODETECT spr round 2 (radius: 10)
[02:41:14 -457206.526483] AUTODETECT spr round 3 (radius: 15)
[02:43:31 -371793.574489] AUTODETECT spr round 4 (radius: 20)
[02:46:04 -323423.029944] AUTODETECT spr round 5 (radius: 25)
[02:49:09 -315709.519803] SPR radius for FAST iterations: 25 (autodetect)
[02:49:09 -315709.519803] Model parameter optimization (eps = 3.000000)
[02:49:27 -315357.134777] FAST spr round 1 (radius: 25)
[02:51:56 -272448.204302] FAST spr round 2 (radius: 25)
[02:53:55 -268597.004013] FAST spr round 3 (radius: 25)
[02:55:42 -268238.955630] FAST spr round 4 (radius: 25)
[02:57:20 -268222.584830] FAST spr round 5 (radius: 25)
[02:58:51 -268220.920786] FAST spr round 6 (radius: 25)
[03:00:19 -268220.919546] Model parameter optimization (eps = 1.000000)
[03:00:32 -268215.238426] SLOW spr round 1 (radius: 5)
[03:02:27 -268171.447105] SLOW spr round 2 (radius: 5)
[03:04:22 -268164.827782] SLOW spr round 3 (radius: 5)
[03:06:12 -268164.808872] SLOW spr round 4 (radius: 10)
[03:08:08 -268164.511656] SLOW spr round 5 (radius: 5)
[03:10:23 -268164.510944] SLOW spr round 6 (radius: 10)
[03:12:26 -268164.510425] SLOW spr round 7 (radius: 15)
[03:15:10 -268164.302676] SLOW spr round 8 (radius: 5)
[03:17:34 -268164.302274] SLOW spr round 9 (radius: 10)
[03:19:44 -268164.301989] SLOW spr round 10 (radius: 15)
[03:22:26 -268164.301750] SLOW spr round 11 (radius: 20)
[03:27:03 -268164.301549] SLOW spr round 12 (radius: 25)
[03:32:33 -268164.301377] Model parameter optimization (eps = 0.100000)

[03:32:41] ML tree search #3, logLikelihood: -268164.185086

[03:32:41 -1007000.204652] Initial branch length optimization
[03:32:45 -816764.971669] Model parameter optimization (eps = 10.000000)
[03:33:31 -814650.684167] AUTODETECT spr round 1 (radius: 5)
[03:35:24 -587759.584594] AUTODETECT spr round 2 (radius: 10)
[03:37:29 -454770.999394] AUTODETECT spr round 3 (radius: 15)
[03:39:47 -358689.989640] AUTODETECT spr round 4 (radius: 20)
[03:42:10 -326097.498203] AUTODETECT spr round 5 (radius: 25)
[03:45:31 -312703.922922] SPR radius for FAST iterations: 25 (autodetect)
[03:45:31 -312703.922922] Model parameter optimization (eps = 3.000000)
[03:45:50 -312270.114895] FAST spr round 1 (radius: 25)
[03:48:17 -270897.455075] FAST spr round 2 (radius: 25)
[03:50:02 -268373.530176] FAST spr round 3 (radius: 25)
[03:51:41 -268286.068860] FAST spr round 4 (radius: 25)
[03:53:13 -268274.146202] FAST spr round 5 (radius: 25)
[03:54:42 -268274.145866] Model parameter optimization (eps = 1.000000)
[03:55:01 -268265.411414] SLOW spr round 1 (radius: 5)
[03:56:56 -268228.741715] SLOW spr round 2 (radius: 5)
[03:58:51 -268223.853448] SLOW spr round 3 (radius: 5)
[04:00:46 -268220.969334] SLOW spr round 4 (radius: 5)
[04:02:36 -268220.969047] SLOW spr round 5 (radius: 10)
[04:04:33 -268220.968960] SLOW spr round 6 (radius: 15)
[04:07:25 -268220.968907] SLOW spr round 7 (radius: 20)
[04:12:12 -268220.968870] SLOW spr round 8 (radius: 25)
[04:18:19 -268220.499916] SLOW spr round 9 (radius: 5)
[04:20:50 -268211.227515] SLOW spr round 10 (radius: 5)
[04:23:01 -268211.226887] SLOW spr round 11 (radius: 10)
[04:25:02 -268211.226760] SLOW spr round 12 (radius: 15)
[04:27:51 -268211.226708] SLOW spr round 13 (radius: 20)
[04:32:50 -268211.226674] SLOW spr round 14 (radius: 25)
[04:39:20 -268211.226647] Model parameter optimization (eps = 0.100000)

[04:39:29] ML tree search #4, logLikelihood: -268210.951612

[04:39:29 -1010675.716433] Initial branch length optimization
[04:39:32 -819340.548100] Model parameter optimization (eps = 10.000000)
[04:40:09 -816798.941200] AUTODETECT spr round 1 (radius: 5)
[04:42:02 -595752.616857] AUTODETECT spr round 2 (radius: 10)
[04:44:07 -450227.809390] AUTODETECT spr round 3 (radius: 15)
[04:46:23 -419219.411007] AUTODETECT spr round 4 (radius: 20)
[04:49:12 -357146.963779] AUTODETECT spr round 5 (radius: 25)
[04:52:18 -324695.796440] SPR radius for FAST iterations: 25 (autodetect)
[04:52:19 -324695.796440] Model parameter optimization (eps = 3.000000)
[04:52:38 -324262.776985] FAST spr round 1 (radius: 25)
[04:54:59 -271907.070015] FAST spr round 2 (radius: 25)
[04:56:47 -268469.324285] FAST spr round 3 (radius: 25)
[04:58:27 -268265.866830] FAST spr round 4 (radius: 25)
[05:00:02 -268246.393505] FAST spr round 5 (radius: 25)
[05:01:32 -268242.077005] FAST spr round 6 (radius: 25)
[05:03:01 -268239.672825] FAST spr round 7 (radius: 25)
[05:04:29 -268239.671859] Model parameter optimization (eps = 1.000000)
[05:04:41 -268235.526368] SLOW spr round 1 (radius: 5)
[05:06:32 -268182.338478] SLOW spr round 2 (radius: 5)
[05:08:24 -268182.102913] SLOW spr round 3 (radius: 5)
[05:10:14 -268182.102772] SLOW spr round 4 (radius: 10)
[05:12:10 -268182.102537] SLOW spr round 5 (radius: 15)
[05:15:00 -268181.783297] SLOW spr round 6 (radius: 5)
[05:17:24 -268181.783224] SLOW spr round 7 (radius: 10)
[05:19:33 -268181.783203] SLOW spr round 8 (radius: 15)
[05:22:17 -268181.783181] SLOW spr round 9 (radius: 20)
[05:28:06 -268181.783159] SLOW spr round 10 (radius: 25)
[05:37:45 -268181.783138] Model parameter optimization (eps = 0.100000)

[05:37:52] ML tree search #5, logLikelihood: -268181.756000

[05:37:52 -993561.192934] Initial branch length optimization
[05:37:58 -808654.793208] Model parameter optimization (eps = 10.000000)
[05:39:21 -806255.125228] AUTODETECT spr round 1 (radius: 5)
[05:42:33 -595924.011477] AUTODETECT spr round 2 (radius: 10)
[05:45:56 -450712.312136] AUTODETECT spr round 3 (radius: 15)
[05:49:39 -365886.775450] AUTODETECT spr round 4 (radius: 20)
[05:53:55 -324837.183563] AUTODETECT spr round 5 (radius: 25)
[05:58:38 -316587.754032] SPR radius for FAST iterations: 25 (autodetect)
[05:58:38 -316587.754032] Model parameter optimization (eps = 3.000000)
[05:59:10 -316239.977470] FAST spr round 1 (radius: 25)
[06:03:03 -270869.493242] FAST spr round 2 (radius: 25)
[06:06:08 -268468.528790] FAST spr round 3 (radius: 25)
[06:08:50 -268303.797366] FAST spr round 4 (radius: 25)
[06:11:14 -268286.462021] FAST spr round 5 (radius: 25)
[06:13:31 -268282.033440] FAST spr round 6 (radius: 25)
[06:15:48 -268281.108045] FAST spr round 7 (radius: 25)
[06:18:02 -268281.107927] Model parameter optimization (eps = 1.000000)
[06:18:24 -268274.944940] SLOW spr round 1 (radius: 5)
[06:21:19 -268204.328252] SLOW spr round 2 (radius: 5)
[06:24:12 -268200.664899] SLOW spr round 3 (radius: 5)
[06:27:05 -268200.615795] SLOW spr round 4 (radius: 10)
[06:30:03 -268200.057770] SLOW spr round 5 (radius: 5)
[06:33:33 -268200.056661] SLOW spr round 6 (radius: 10)
[06:36:43 -268188.859892] SLOW spr round 7 (radius: 5)
[06:40:11 -268187.276240] SLOW spr round 8 (radius: 5)
[06:43:18 -268186.434912] SLOW spr round 9 (radius: 5)
[06:46:14 -268186.433403] SLOW spr round 10 (radius: 10)
[06:49:12 -268186.432726] SLOW spr round 11 (radius: 15)
[06:53:36 -268186.432367] SLOW spr round 12 (radius: 20)
[07:01:27 -268186.432170] SLOW spr round 13 (radius: 25)
[07:11:42 -268186.432057] Model parameter optimization (eps = 0.100000)

[07:11:55] ML tree search #6, logLikelihood: -268186.234051

[07:11:55 -1006590.761384] Initial branch length optimization
[07:12:00 -816108.183434] Model parameter optimization (eps = 10.000000)
[07:13:03 -814002.051932] AUTODETECT spr round 1 (radius: 5)
[07:16:04 -601049.871560] AUTODETECT spr round 2 (radius: 10)
[07:19:17 -452897.722158] AUTODETECT spr round 3 (radius: 15)
[07:22:45 -385340.309200] AUTODETECT spr round 4 (radius: 20)
[07:27:11 -328376.645175] AUTODETECT spr round 5 (radius: 25)
[07:31:56 -319756.740942] SPR radius for FAST iterations: 25 (autodetect)
[07:31:56 -319756.740942] Model parameter optimization (eps = 3.000000)
[07:32:24 -319324.936879] FAST spr round 1 (radius: 25)
[07:36:25 -270881.448879] FAST spr round 2 (radius: 25)
[07:39:30 -268451.087726] FAST spr round 3 (radius: 25)
[07:42:07 -268306.190180] FAST spr round 4 (radius: 25)
[07:44:32 -268274.763854] FAST spr round 5 (radius: 25)
[07:46:52 -268269.817514] FAST spr round 6 (radius: 25)
[07:49:07 -268269.817316] Model parameter optimization (eps = 1.000000)
[07:49:28 -268265.056620] SLOW spr round 1 (radius: 5)
[07:52:28 -268190.206074] SLOW spr round 2 (radius: 5)
[07:55:26 -268184.884167] SLOW spr round 3 (radius: 5)
[07:58:18 -268184.883792] SLOW spr round 4 (radius: 10)
[08:01:16 -268183.673010] SLOW spr round 5 (radius: 5)
[08:04:48 -268182.476472] SLOW spr round 6 (radius: 5)
[08:07:55 -268182.476238] SLOW spr round 7 (radius: 10)
[08:10:55 -268182.476093] SLOW spr round 8 (radius: 15)
[08:15:14 -268182.475971] SLOW spr round 9 (radius: 20)
[08:22:23 -268182.475862] SLOW spr round 10 (radius: 25)
[08:31:41 -268182.475764] Model parameter optimization (eps = 0.100000)

[08:31:51] ML tree search #7, logLikelihood: -268182.448421

[08:31:51 -1007354.977008] Initial branch length optimization
[08:31:58 -814012.323339] Model parameter optimization (eps = 10.000000)
[08:33:22 -811943.462469] AUTODETECT spr round 1 (radius: 5)
[08:36:23 -591940.798754] AUTODETECT spr round 2 (radius: 10)
[08:39:38 -420320.041893] AUTODETECT spr round 3 (radius: 15)
[08:43:09 -340011.053901] AUTODETECT spr round 4 (radius: 20)
[08:47:26 -315101.203747] AUTODETECT spr round 5 (radius: 25)
[08:52:37 -308261.931595] SPR radius for FAST iterations: 25 (autodetect)
[08:52:37 -308261.931595] Model parameter optimization (eps = 3.000000)
[08:53:09 -307866.441687] FAST spr round 1 (radius: 25)
[08:57:08 -269642.068058] FAST spr round 2 (radius: 25)
[09:00:12 -268456.191139] FAST spr round 3 (radius: 25)
[09:02:46 -268320.561376] FAST spr round 4 (radius: 25)
[09:05:13 -268302.889367] FAST spr round 5 (radius: 25)
[09:07:33 -268291.020809] FAST spr round 6 (radius: 25)
[09:09:48 -268291.006492] Model parameter optimization (eps = 1.000000)
[09:10:16 -268286.668206] SLOW spr round 1 (radius: 5)
[09:13:23 -268216.451866] SLOW spr round 2 (radius: 5)
[09:16:25 -268215.886270] SLOW spr round 3 (radius: 5)
[09:19:21 -268215.885758] SLOW spr round 4 (radius: 10)
[09:22:26 -268215.622460] SLOW spr round 5 (radius: 5)
[09:25:54 -268215.622329] SLOW spr round 6 (radius: 10)
[09:29:03 -268215.622277] SLOW spr round 7 (radius: 15)
[09:33:13 -268215.622238] SLOW spr round 8 (radius: 20)
[09:40:21 -268215.622205] SLOW spr round 9 (radius: 25)
[09:49:26 -268215.622174] Model parameter optimization (eps = 0.100000)

[09:49:45] ML tree search #8, logLikelihood: -268215.225400

[09:49:45 -1008815.201288] Initial branch length optimization
[09:49:51 -817501.060938] Model parameter optimization (eps = 10.000000)
[09:51:04 -815317.900450] AUTODETECT spr round 1 (radius: 5)
[09:54:07 -593617.434250] AUTODETECT spr round 2 (radius: 10)
[09:57:21 -444150.613191] AUTODETECT spr round 3 (radius: 15)
[10:00:59 -375621.394042] AUTODETECT spr round 4 (radius: 20)
[10:04:55 -343924.883014] AUTODETECT spr round 5 (radius: 25)
[10:09:56 -320786.507314] SPR radius for FAST iterations: 25 (autodetect)
[10:09:56 -320786.507314] Model parameter optimization (eps = 3.000000)
[10:10:36 -320294.509519] FAST spr round 1 (radius: 25)
[10:14:49 -270972.829244] FAST spr round 2 (radius: 25)
[10:17:59 -268495.225520] FAST spr round 3 (radius: 25)
[10:20:46 -268338.265367] FAST spr round 4 (radius: 25)
[10:23:17 -268298.123138] FAST spr round 5 (radius: 25)
[10:25:38 -268256.009434] FAST spr round 6 (radius: 25)
[10:27:54 -268256.009237] Model parameter optimization (eps = 1.000000)
[10:28:11 -268251.016781] SLOW spr round 1 (radius: 5)
[10:31:13 -268191.600678] SLOW spr round 2 (radius: 5)
[10:34:08 -268189.618199] SLOW spr round 3 (radius: 5)
[10:36:59 -268189.599043] SLOW spr round 4 (radius: 10)
[10:39:57 -268189.359886] SLOW spr round 5 (radius: 5)
[10:43:30 -268189.358331] SLOW spr round 6 (radius: 10)
[10:46:39 -268189.357278] SLOW spr round 7 (radius: 15)
[10:50:49 -268189.356440] SLOW spr round 8 (radius: 20)
[10:57:34 -268189.355768] SLOW spr round 9 (radius: 25)
[11:06:35 -268189.355226] Model parameter optimization (eps = 0.100000)

[11:06:46] ML tree search #9, logLikelihood: -268189.219678

[11:06:47 -1002193.779971] Initial branch length optimization
[11:06:51 -812744.616249] Model parameter optimization (eps = 10.000000)
[11:07:58 -810508.032351] AUTODETECT spr round 1 (radius: 5)
[11:11:00 -595219.827636] AUTODETECT spr round 2 (radius: 10)
[11:14:14 -445786.248932] AUTODETECT spr round 3 (radius: 15)
[11:17:46 -365473.684233] AUTODETECT spr round 4 (radius: 20)
[11:21:34 -338637.750072] AUTODETECT spr round 5 (radius: 25)
[11:26:12 -317032.582695] SPR radius for FAST iterations: 25 (autodetect)
[11:26:12 -317032.582695] Model parameter optimization (eps = 3.000000)
[11:26:39 -316578.153004] FAST spr round 1 (radius: 25)
[11:30:31 -270911.707429] FAST spr round 2 (radius: 25)
[11:33:23 -268571.754415] FAST spr round 3 (radius: 25)
[11:36:07 -268278.349568] FAST spr round 4 (radius: 25)
[11:38:31 -268270.218954] FAST spr round 5 (radius: 25)
[11:40:50 -268269.887397] FAST spr round 6 (radius: 25)
[11:43:06 -268269.887309] Model parameter optimization (eps = 1.000000)
[11:43:24 -268267.466637] SLOW spr round 1 (radius: 5)
[11:46:23 -268194.114580] SLOW spr round 2 (radius: 5)
[11:49:16 -268190.594437] SLOW spr round 3 (radius: 5)
[11:52:06 -268190.594038] SLOW spr round 4 (radius: 10)
[11:55:03 -268190.593957] SLOW spr round 5 (radius: 15)
[11:59:27 -268190.385381] SLOW spr round 6 (radius: 5)
[12:03:11 -268190.385305] SLOW spr round 7 (radius: 10)
[12:06:28 -268190.385273] SLOW spr round 8 (radius: 15)
[12:09:37 -268190.385244] SLOW spr round 9 (radius: 20)
[12:14:34 -268190.385216] SLOW spr round 10 (radius: 25)
[12:20:55 -268190.385189] Model parameter optimization (eps = 0.100000)

[12:21:00] ML tree search #10, logLikelihood: -268190.336674

[12:21:00 -1003990.060159] Initial branch length optimization
[12:21:04 -809520.171223] Model parameter optimization (eps = 10.000000)
[12:21:53 -807371.125145] AUTODETECT spr round 1 (radius: 5)
[12:23:47 -589239.555482] AUTODETECT spr round 2 (radius: 10)
[12:25:49 -462706.472830] AUTODETECT spr round 3 (radius: 15)
[12:28:11 -360255.827107] AUTODETECT spr round 4 (radius: 20)
[12:30:54 -315724.750569] AUTODETECT spr round 5 (radius: 25)
[12:34:28 -312151.533249] SPR radius for FAST iterations: 25 (autodetect)
[12:34:28 -312151.533249] Model parameter optimization (eps = 3.000000)
[12:34:47 -311702.189434] FAST spr round 1 (radius: 25)
[12:37:09 -270078.834720] FAST spr round 2 (radius: 25)
[12:38:56 -268400.760097] FAST spr round 3 (radius: 25)
[12:40:38 -268318.078772] FAST spr round 4 (radius: 25)
[12:42:15 -268273.860188] FAST spr round 5 (radius: 25)
[12:43:45 -268272.488702] FAST spr round 6 (radius: 25)
[12:45:13 -268272.487017] Model parameter optimization (eps = 1.000000)
[12:45:27 -268269.222003] SLOW spr round 1 (radius: 5)
[12:47:21 -268208.458553] SLOW spr round 2 (radius: 5)
[12:49:14 -268198.869138] SLOW spr round 3 (radius: 5)
[12:51:06 -268196.654515] SLOW spr round 4 (radius: 5)
[12:52:55 -268196.654300] SLOW spr round 5 (radius: 10)
[12:54:51 -268196.654210] SLOW spr round 6 (radius: 15)
[12:57:43 -268196.654173] SLOW spr round 7 (radius: 20)
[13:02:25 -268196.654147] SLOW spr round 8 (radius: 25)
[13:08:24 -268196.654126] Model parameter optimization (eps = 0.100000)

[13:08:33] ML tree search #11, logLikelihood: -268196.522770

[13:08:33 -1001738.929514] Initial branch length optimization
[13:08:39 -814007.152972] Model parameter optimization (eps = 10.000000)
[13:09:23 -811802.979952] AUTODETECT spr round 1 (radius: 5)
[13:11:18 -592911.753163] AUTODETECT spr round 2 (radius: 10)
[13:13:20 -439968.229889] AUTODETECT spr round 3 (radius: 15)
[13:15:29 -361233.731065] AUTODETECT spr round 4 (radius: 20)
[13:17:57 -329790.221884] AUTODETECT spr round 5 (radius: 25)
[13:21:12 -312097.567353] SPR radius for FAST iterations: 25 (autodetect)
[13:21:12 -312097.567353] Model parameter optimization (eps = 3.000000)
[13:21:31 -311706.751080] FAST spr round 1 (radius: 25)
[13:23:46 -270166.452573] FAST spr round 2 (radius: 25)
[13:25:34 -268418.396336] FAST spr round 3 (radius: 25)
[13:27:13 -268327.150065] FAST spr round 4 (radius: 25)
[13:28:45 -268321.193157] FAST spr round 5 (radius: 25)
[13:30:14 -268321.192935] Model parameter optimization (eps = 1.000000)
[13:30:27 -268318.377375] SLOW spr round 1 (radius: 5)
[13:32:21 -268262.021220] SLOW spr round 2 (radius: 5)
[13:34:14 -268255.502908] SLOW spr round 3 (radius: 5)
[13:36:06 -268255.502515] SLOW spr round 4 (radius: 10)
[13:38:01 -268255.316032] SLOW spr round 5 (radius: 5)
[13:40:19 -268237.696336] SLOW spr round 6 (radius: 5)
[13:42:23 -268218.181418] SLOW spr round 7 (radius: 5)
[13:44:17 -268218.181139] SLOW spr round 8 (radius: 10)
[13:46:14 -268218.181101] SLOW spr round 9 (radius: 15)
[13:49:03 -268218.181071] SLOW spr round 10 (radius: 20)
[13:53:45 -268218.181043] SLOW spr round 11 (radius: 25)
[13:59:47 -268218.181016] Model parameter optimization (eps = 0.100000)

[13:59:55] ML tree search #12, logLikelihood: -268217.960217

[13:59:55 -994411.839390] Initial branch length optimization
[13:59:59 -810571.631138] Model parameter optimization (eps = 10.000000)
[14:00:46 -808320.981130] AUTODETECT spr round 1 (radius: 5)
[14:02:41 -605136.326349] AUTODETECT spr round 2 (radius: 10)
[14:04:46 -426588.920837] AUTODETECT spr round 3 (radius: 15)
[14:07:02 -351060.102715] AUTODETECT spr round 4 (radius: 20)
[14:09:31 -328461.806159] AUTODETECT spr round 5 (radius: 25)
[14:12:53 -310608.021141] SPR radius for FAST iterations: 25 (autodetect)
[14:12:53 -310608.021141] Model parameter optimization (eps = 3.000000)
[14:13:12 -310252.503529] FAST spr round 1 (radius: 25)
[14:15:39 -270717.783466] FAST spr round 2 (radius: 25)
[14:17:33 -268381.748640] FAST spr round 3 (radius: 25)
[14:19:14 -268297.774399] FAST spr round 4 (radius: 25)
[14:20:48 -268290.188385] FAST spr round 5 (radius: 25)
[14:22:18 -268290.188011] Model parameter optimization (eps = 1.000000)
[14:22:31 -268285.489278] SLOW spr round 1 (radius: 5)
[14:24:26 -268202.450969] SLOW spr round 2 (radius: 5)
[14:26:19 -268183.199956] SLOW spr round 3 (radius: 5)
[14:28:12 -268182.813033] SLOW spr round 4 (radius: 5)
[14:30:02 -268179.255946] SLOW spr round 5 (radius: 5)
[14:31:51 -268179.255384] SLOW spr round 6 (radius: 10)
[14:33:47 -268171.488669] SLOW spr round 7 (radius: 5)
[14:36:05 -268166.990080] SLOW spr round 8 (radius: 5)
[14:38:06 -268166.989316] SLOW spr round 9 (radius: 10)
[14:40:06 -268166.989087] SLOW spr round 10 (radius: 15)
[14:42:56 -268166.988955] SLOW spr round 11 (radius: 20)
[14:47:39 -268166.988856] SLOW spr round 12 (radius: 25)
[14:53:41 -268159.721548] SLOW spr round 13 (radius: 5)
[14:56:12 -268157.893919] SLOW spr round 14 (radius: 5)
[14:58:22 -268157.891832] SLOW spr round 15 (radius: 10)
[15:00:24 -268157.890627] SLOW spr round 16 (radius: 15)
[15:03:12 -268157.889917] SLOW spr round 17 (radius: 20)
[15:08:05 -268157.889491] SLOW spr round 18 (radius: 25)
[15:14:26 -268157.889227] Model parameter optimization (eps = 0.100000)

[15:14:31] ML tree search #13, logLikelihood: -268157.844231

[15:14:31 -1006364.888467] Initial branch length optimization
[15:14:35 -815010.027273] Model parameter optimization (eps = 10.000000)
[15:15:25 -812657.928520] AUTODETECT spr round 1 (radius: 5)
[15:17:20 -579609.801394] AUTODETECT spr round 2 (radius: 10)
[15:19:22 -455204.141130] AUTODETECT spr round 3 (radius: 15)
[15:21:44 -368838.301088] AUTODETECT spr round 4 (radius: 20)
[15:24:12 -321651.671065] AUTODETECT spr round 5 (radius: 25)
[15:27:17 -315109.186966] SPR radius for FAST iterations: 25 (autodetect)
[15:27:17 -315109.186966] Model parameter optimization (eps = 3.000000)
[15:27:34 -314702.982011] FAST spr round 1 (radius: 25)
[15:30:02 -271536.605753] FAST spr round 2 (radius: 25)
[15:32:03 -269596.507791] FAST spr round 3 (radius: 25)
[15:33:50 -269478.336055] FAST spr round 4 (radius: 25)
[15:35:23 -269456.539438] FAST spr round 5 (radius: 25)
[15:36:53 -269456.538924] Model parameter optimization (eps = 1.000000)
[15:37:10 -269446.800087] SLOW spr round 1 (radius: 5)
[15:39:10 -269369.736259] SLOW spr round 2 (radius: 5)
[15:41:08 -269362.511100] SLOW spr round 3 (radius: 5)
[15:43:01 -269360.368007] SLOW spr round 4 (radius: 5)
[15:44:52 -269359.854408] SLOW spr round 5 (radius: 5)
[15:46:41 -269359.854309] SLOW spr round 6 (radius: 10)
[15:48:38 -269358.634790] SLOW spr round 7 (radius: 5)
[15:50:56 -269358.130964] SLOW spr round 8 (radius: 5)
[15:52:58 -269358.130777] SLOW spr round 9 (radius: 10)
[15:54:57 -269358.130650] SLOW spr round 10 (radius: 15)
[15:57:41 -269358.130546] SLOW spr round 11 (radius: 20)
[16:02:04 -269297.486357] SLOW spr round 12 (radius: 5)
[16:04:42 -269112.376287] SLOW spr round 13 (radius: 5)
[16:06:58 -268212.013253] SLOW spr round 14 (radius: 5)
[16:09:02 -268163.714535] SLOW spr round 15 (radius: 5)
[16:10:55 -268163.712922] SLOW spr round 16 (radius: 10)
[16:12:52 -268163.712253] SLOW spr round 17 (radius: 15)
[16:15:46 -268163.711634] SLOW spr round 18 (radius: 20)
[16:20:39 -268163.711463] SLOW spr round 19 (radius: 25)
[16:26:57 -268155.768058] SLOW spr round 20 (radius: 5)
[16:29:28 -268153.359760] SLOW spr round 21 (radius: 5)
[16:31:37 -268153.359593] SLOW spr round 22 (radius: 10)
[16:33:37 -268153.359524] SLOW spr round 23 (radius: 15)
[16:36:27 -268153.359484] SLOW spr round 24 (radius: 20)
[16:41:33 -268153.359455] SLOW spr round 25 (radius: 25)
[16:48:18 -268153.359432] Model parameter optimization (eps = 0.100000)

[16:48:31] ML tree search #14, logLikelihood: -268152.519180

[16:48:31 -997073.673896] Initial branch length optimization
[16:48:36 -813302.289190] Model parameter optimization (eps = 10.000000)
[16:49:22 -810945.094478] AUTODETECT spr round 1 (radius: 5)
[16:51:15 -594307.286941] AUTODETECT spr round 2 (radius: 10)
[16:53:16 -452471.823631] AUTODETECT spr round 3 (radius: 15)
[16:55:30 -350529.485392] AUTODETECT spr round 4 (radius: 20)
[16:57:57 -320825.520363] AUTODETECT spr round 5 (radius: 25)
[17:01:11 -312932.751459] SPR radius for FAST iterations: 25 (autodetect)
[17:01:11 -312932.751459] Model parameter optimization (eps = 3.000000)
[17:01:31 -312576.553741] FAST spr round 1 (radius: 25)
[17:03:59 -270112.686052] FAST spr round 2 (radius: 25)
[17:05:58 -268355.086599] FAST spr round 3 (radius: 25)
[17:07:39 -268244.934910] FAST spr round 4 (radius: 25)
[17:09:15 -268229.835254] FAST spr round 5 (radius: 25)
[17:10:44 -268229.834101] Model parameter optimization (eps = 1.000000)
[17:10:57 -268219.047593] SLOW spr round 1 (radius: 5)
[17:12:53 -268159.644763] SLOW spr round 2 (radius: 5)
[17:14:48 -268157.197181] SLOW spr round 3 (radius: 5)
[17:16:38 -268157.196650] SLOW spr round 4 (radius: 10)
[17:18:34 -268157.196355] SLOW spr round 5 (radius: 15)
[17:21:24 -268157.196104] SLOW spr round 6 (radius: 20)
[17:26:13 -268157.195883] SLOW spr round 7 (radius: 25)
[17:32:43 -268157.195684] Model parameter optimization (eps = 0.100000)

[17:32:47] ML tree search #15, logLikelihood: -268157.159708

[17:32:47 -1009871.844154] Initial branch length optimization
[17:32:51 -816363.714576] Model parameter optimization (eps = 10.000000)
[17:33:44 -814184.258751] AUTODETECT spr round 1 (radius: 5)
[17:35:39 -595597.985817] AUTODETECT spr round 2 (radius: 10)
[17:37:41 -468714.335874] AUTODETECT spr round 3 (radius: 15)
[17:39:58 -371701.973946] AUTODETECT spr round 4 (radius: 20)
[17:42:27 -340524.707319] AUTODETECT spr round 5 (radius: 25)
[17:45:27 -328856.787605] SPR radius for FAST iterations: 25 (autodetect)
[17:45:27 -328856.787605] Model parameter optimization (eps = 3.000000)
[17:45:46 -328412.001050] FAST spr round 1 (radius: 25)
[17:48:29 -270381.403414] FAST spr round 2 (radius: 25)
[17:50:30 -268427.189820] FAST spr round 3 (radius: 25)
[17:52:18 -268329.160403] FAST spr round 4 (radius: 25)
[17:53:58 -268304.665623] FAST spr round 5 (radius: 25)
[17:55:29 -268295.419877] FAST spr round 6 (radius: 25)
[17:56:57 -268295.419094] Model parameter optimization (eps = 1.000000)
[17:57:09 -268291.586397] SLOW spr round 1 (radius: 5)
[17:59:10 -268221.888800] SLOW spr round 2 (radius: 5)
[18:01:09 -268208.430496] SLOW spr round 3 (radius: 5)
[18:03:02 -268206.617295] SLOW spr round 4 (radius: 5)
[18:04:52 -268206.617002] SLOW spr round 5 (radius: 10)
[18:06:48 -268206.407656] SLOW spr round 6 (radius: 5)
[18:09:06 -268206.407406] SLOW spr round 7 (radius: 10)
[18:11:09 -268206.407343] SLOW spr round 8 (radius: 15)
[18:13:56 -268200.524526] SLOW spr round 9 (radius: 5)
[18:16:22 -268200.049987] SLOW spr round 10 (radius: 5)
[18:18:30 -268200.049861] SLOW spr round 11 (radius: 10)
[18:20:29 -268200.049809] SLOW spr round 12 (radius: 15)
[18:23:18 -268200.049758] SLOW spr round 13 (radius: 20)
[18:27:58 -268200.049706] SLOW spr round 14 (radius: 25)
[18:33:39 -268200.049654] Model parameter optimization (eps = 0.100000)

[18:33:47] ML tree search #16, logLikelihood: -268199.604083

[18:33:47 -1005032.955670] Initial branch length optimization
[18:33:51 -815535.196060] Model parameter optimization (eps = 10.000000)
[18:34:33 -813421.749464] AUTODETECT spr round 1 (radius: 5)
[18:36:30 -596456.054507] AUTODETECT spr round 2 (radius: 10)
[18:38:33 -434973.955783] AUTODETECT spr round 3 (radius: 15)
[18:40:49 -350226.131978] AUTODETECT spr round 4 (radius: 20)
[18:43:37 -314900.231582] AUTODETECT spr round 5 (radius: 25)
[18:46:52 -306700.587633] SPR radius for FAST iterations: 25 (autodetect)
[18:46:52 -306700.587633] Model parameter optimization (eps = 3.000000)
[18:47:10 -306239.756143] FAST spr round 1 (radius: 25)
[18:49:30 -270009.374082] FAST spr round 2 (radius: 25)
[18:51:19 -268452.292524] FAST spr round 3 (radius: 25)
[18:53:00 -268338.963411] FAST spr round 4 (radius: 25)
[18:54:35 -268329.482222] FAST spr round 5 (radius: 25)
[18:56:06 -268329.482105] Model parameter optimization (eps = 1.000000)
[18:56:20 -268325.903890] SLOW spr round 1 (radius: 5)
[18:58:16 -268252.651726] SLOW spr round 2 (radius: 5)
[19:00:10 -268243.785689] SLOW spr round 3 (radius: 5)
[19:02:02 -268243.785400] SLOW spr round 4 (radius: 10)
[19:04:00 -268238.207696] SLOW spr round 5 (radius: 5)
[19:06:17 -268238.207570] SLOW spr round 6 (radius: 10)
[19:08:20 -268238.207516] SLOW spr round 7 (radius: 15)
[19:11:07 -268237.011323] SLOW spr round 8 (radius: 5)
[19:13:34 -268236.964726] SLOW spr round 9 (radius: 10)
[19:15:44 -268236.964576] SLOW spr round 10 (radius: 15)
[19:18:29 -268236.964520] SLOW spr round 11 (radius: 20)
[19:23:12 -268235.618291] SLOW spr round 12 (radius: 5)
[19:25:40 -268211.305506] SLOW spr round 13 (radius: 5)
[19:27:50 -268211.305189] SLOW spr round 14 (radius: 10)
[19:29:50 -268211.305112] SLOW spr round 15 (radius: 15)
[19:32:39 -268211.305054] SLOW spr round 16 (radius: 20)
[19:37:18 -268211.304999] SLOW spr round 17 (radius: 25)
[19:43:26 -268211.304943] Model parameter optimization (eps = 0.100000)

[19:43:39] ML tree search #17, logLikelihood: -268210.244671

[19:43:39 -1002085.530175] Initial branch length optimization
[19:43:43 -814656.516764] Model parameter optimization (eps = 10.000000)
[19:44:18 -812516.370120] AUTODETECT spr round 1 (radius: 5)
[19:46:13 -601161.541948] AUTODETECT spr round 2 (radius: 10)
[19:48:15 -469382.587718] AUTODETECT spr round 3 (radius: 15)
[19:50:29 -368323.593775] AUTODETECT spr round 4 (radius: 20)
[19:52:53 -345298.306219] AUTODETECT spr round 5 (radius: 25)
[19:56:19 -323742.139672] SPR radius for FAST iterations: 25 (autodetect)
[19:56:19 -323742.139672] Model parameter optimization (eps = 3.000000)
[19:56:43 -323381.752461] FAST spr round 1 (radius: 25)
[19:59:13 -271887.709852] FAST spr round 2 (radius: 25)
[20:01:07 -268500.493743] FAST spr round 3 (radius: 25)
[20:02:50 -268276.882149] FAST spr round 4 (radius: 25)
[20:04:25 -268235.946318] FAST spr round 5 (radius: 25)
[20:05:56 -268234.499114] FAST spr round 6 (radius: 25)
[20:07:25 -268234.498604] Model parameter optimization (eps = 1.000000)
[20:07:37 -268231.148328] SLOW spr round 1 (radius: 5)
[20:09:33 -268179.718111] SLOW spr round 2 (radius: 5)
[20:11:25 -268175.192980] SLOW spr round 3 (radius: 5)
[20:13:16 -268175.192573] SLOW spr round 4 (radius: 10)
[20:15:11 -268175.192496] SLOW spr round 5 (radius: 15)
[20:18:02 -268175.192430] SLOW spr round 6 (radius: 20)
[20:22:45 -268175.192365] SLOW spr round 7 (radius: 25)
[20:28:51 -268175.192299] Model parameter optimization (eps = 0.100000)

[20:28:56] ML tree search #18, logLikelihood: -268175.168527

[20:28:56 -1000335.287714] Initial branch length optimization
[20:29:02 -813359.778284] Model parameter optimization (eps = 10.000000)
[20:29:47 -811139.859170] AUTODETECT spr round 1 (radius: 5)
[20:31:41 -594425.489455] AUTODETECT spr round 2 (radius: 10)
[20:33:43 -447820.773637] AUTODETECT spr round 3 (radius: 15)
[20:35:54 -366519.256671] AUTODETECT spr round 4 (radius: 20)
[20:38:21 -332903.279766] AUTODETECT spr round 5 (radius: 25)
[20:41:52 -321849.458535] SPR radius for FAST iterations: 25 (autodetect)
[20:41:52 -321849.458535] Model parameter optimization (eps = 3.000000)
[20:42:01 -321827.947172] FAST spr round 1 (radius: 25)
[20:44:48 -270744.578722] FAST spr round 2 (radius: 25)
[20:46:45 -268784.935036] FAST spr round 3 (radius: 25)
[20:48:26 -268632.528394] FAST spr round 4 (radius: 25)
[20:49:58 -268623.728673] FAST spr round 5 (radius: 25)
[20:51:27 -268623.727410] Model parameter optimization (eps = 1.000000)
[20:51:43 -268313.856697] SLOW spr round 1 (radius: 5)
[20:53:40 -268262.578191] SLOW spr round 2 (radius: 5)
[20:55:33 -268259.126707] SLOW spr round 3 (radius: 5)
[20:57:23 -268259.125940] SLOW spr round 4 (radius: 10)
[20:59:18 -268259.125811] SLOW spr round 5 (radius: 15)
[21:02:06 -268258.630220] SLOW spr round 6 (radius: 5)
[21:04:30 -268258.630062] SLOW spr round 7 (radius: 10)
[21:06:38 -268258.630033] SLOW spr round 8 (radius: 15)
[21:09:21 -268258.630007] SLOW spr round 9 (radius: 20)
[21:13:54 -268226.505184] SLOW spr round 10 (radius: 5)
[21:16:27 -268181.348785] SLOW spr round 11 (radius: 5)
[21:18:38 -268179.151898] SLOW spr round 12 (radius: 5)
[21:20:36 -268179.150963] SLOW spr round 13 (radius: 10)
[21:22:33 -268179.150638] SLOW spr round 14 (radius: 15)
[21:25:26 -268179.150500] SLOW spr round 15 (radius: 20)
[21:30:04 -268179.150435] SLOW spr round 16 (radius: 25)
[21:36:03 -268179.150396] Model parameter optimization (eps = 0.100000)

[21:36:09] ML tree search #19, logLikelihood: -268179.103708

[21:36:09 -1000500.588106] Initial branch length optimization
[21:36:13 -812859.485812] Model parameter optimization (eps = 10.000000)
[21:37:02 -810542.161817] AUTODETECT spr round 1 (radius: 5)
[21:38:57 -593820.932842] AUTODETECT spr round 2 (radius: 10)
[21:41:02 -445990.378883] AUTODETECT spr round 3 (radius: 15)
[21:43:15 -369240.600990] AUTODETECT spr round 4 (radius: 20)
[21:45:43 -335824.438421] AUTODETECT spr round 5 (radius: 25)
[21:48:37 -326797.985143] SPR radius for FAST iterations: 25 (autodetect)
[21:48:37 -326797.985143] Model parameter optimization (eps = 3.000000)
[21:49:04 -326386.918428] FAST spr round 1 (radius: 25)
[21:51:45 -273214.333595] FAST spr round 2 (radius: 25)
[21:53:47 -269108.227291] FAST spr round 3 (radius: 25)
[21:55:34 -268401.190107] FAST spr round 4 (radius: 25)
[21:57:11 -268267.934712] FAST spr round 5 (radius: 25)
[21:58:44 -268258.438468] FAST spr round 6 (radius: 25)
[22:00:12 -268258.411585] Model parameter optimization (eps = 1.000000)
[22:00:25 -268248.284818] SLOW spr round 1 (radius: 5)
[22:02:22 -268196.569280] SLOW spr round 2 (radius: 5)
[22:04:16 -268192.414462] SLOW spr round 3 (radius: 5)
[22:06:07 -268192.411848] SLOW spr round 4 (radius: 10)
[22:08:03 -268192.410527] SLOW spr round 5 (radius: 15)
[22:10:52 -268192.409978] SLOW spr round 6 (radius: 20)
[22:15:30 -268192.409676] SLOW spr round 7 (radius: 25)
[22:21:32 -268192.409506] Model parameter optimization (eps = 0.100000)

[22:21:43] ML tree search #20, logLikelihood: -268192.358282


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.158814,0.402471) (0.168182,0.495623) (0.389042,0.892979) (0.283962,1.779535) 
   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: -268152.519180

AIC score: 540315.038361 / AICc score: 8584375.038361 / BIC score: 549062.909708
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=580).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UHX3/3_mltree/Q9UHX3.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UHX3/3_mltree/Q9UHX3.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UHX3/3_mltree/Q9UHX3.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UHX3/3_mltree/Q9UHX3.raxml.log

Analysis started: 03-Jul-2021 00:06:39 / finished: 03-Jul-2021 22:28:23

Elapsed time: 80503.747 seconds

Consumed energy: 6846.395 Wh (= 34 km in an electric car, or 171 km with an e-scooter!)