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 14-Jul-2021 15:18:34 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UL68/2_msa/Q9UL68_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UL68/3_mltree/Q9UL68 --seed 2 --threads 9 --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 (9 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UL68/2_msa/Q9UL68_trimmed_msa.fasta
[00:00:00] Loaded alignment with 532 taxa and 1207 sites

WARNING: Sequences tr_G3S784_G3S784_GORGO_9595 and sp_Q9UL68_MYT1L_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A226NE01_A0A226NE01_CALSU_9009 and tr_A0A226NTF0_A0A226NTF0_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0SGT0_A0A2D0SGT0_ICTPU_7998 and tr_A0A2D0SHG6_A0A2D0SHG6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SGT5_A0A2D0SGT5_ICTPU_7998 and tr_A0A2D0SHG3_A0A2D0SHG3_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0SGT5_A0A2D0SGT5_ICTPU_7998 and tr_A0A2D0SI20_A0A2D0SI20_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2K5NQN7_A0A2K5NQN7_CERAT_9531 and tr_A0A2K5ZLD1_A0A2K5ZLD1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2K6ECG8_A0A2K6ECG8_MACNE_9545 and tr_A0A2K5YTQ3_A0A2K5YTQ3_MANLE_9568 are exactly identical!
WARNING: Duplicate sequences found: 7

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/Q9UL68/3_mltree/Q9UL68.raxml.reduced.phy

Alignment comprises 1 partitions and 1207 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 1207 / 1207
Gaps: 36.05 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UL68/3_mltree/Q9UL68.raxml.rba

Parallelization scheme autoconfig: 1 worker(s) x 9 thread(s)

Parallel reduction/worker buffer size: 1 KB  / 0 KB

[00:00:00] Generating 20 random starting tree(s) with 532 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 135 / 10800
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -701647.173169] Initial branch length optimization
[00:00:03 -570949.006618] Model parameter optimization (eps = 10.000000)
[00:00:57 -568515.466684] AUTODETECT spr round 1 (radius: 5)
[00:01:38 -391026.752543] AUTODETECT spr round 2 (radius: 10)
[00:02:29 -291026.875831] AUTODETECT spr round 3 (radius: 15)
[00:03:24 -249814.079950] AUTODETECT spr round 4 (radius: 20)
[00:04:35 -234159.531103] AUTODETECT spr round 5 (radius: 25)
[00:05:59 -233894.748357] SPR radius for FAST iterations: 25 (autodetect)
[00:05:59 -233894.748357] Model parameter optimization (eps = 3.000000)
[00:06:24 -233116.295999] FAST spr round 1 (radius: 25)
[00:08:21 -210221.835363] FAST spr round 2 (radius: 25)
[00:09:45 -209557.558523] FAST spr round 3 (radius: 25)
[00:10:28 -209479.081654] FAST spr round 4 (radius: 25)
[00:11:12 -209378.261408] FAST spr round 5 (radius: 25)
[00:11:50 -209368.239653] FAST spr round 6 (radius: 25)
[00:12:26 -209365.374201] FAST spr round 7 (radius: 25)
[00:13:00 -209365.371523] Model parameter optimization (eps = 1.000000)
[00:13:15 -209350.443717] SLOW spr round 1 (radius: 5)
[00:14:07 -209339.376130] SLOW spr round 2 (radius: 5)
[00:14:57 -209339.374995] SLOW spr round 3 (radius: 10)
[00:15:53 -209335.239731] SLOW spr round 4 (radius: 5)
[00:16:59 -209335.188695] SLOW spr round 5 (radius: 10)
[00:18:02 -209334.574450] SLOW spr round 6 (radius: 5)
[00:19:08 -209334.425195] SLOW spr round 7 (radius: 5)
[00:20:05 -209334.424239] SLOW spr round 8 (radius: 10)
[00:21:03 -209334.423938] SLOW spr round 9 (radius: 15)
[00:22:45 -209330.685749] SLOW spr round 10 (radius: 5)
[00:23:56 -209330.618126] SLOW spr round 11 (radius: 10)
[00:25:02 -209330.614339] SLOW spr round 12 (radius: 15)
[00:26:42 -209330.612863] SLOW spr round 13 (radius: 20)
[00:29:25 -209330.570561] SLOW spr round 14 (radius: 25)
[00:32:44 -209330.569504] Model parameter optimization (eps = 0.100000)

[00:32:52] ML tree search #1, logLikelihood: -209330.296036

[00:32:52 -704560.277506] Initial branch length optimization
[00:32:55 -574923.395989] Model parameter optimization (eps = 10.000000)
[00:33:45 -572147.896770] AUTODETECT spr round 1 (radius: 5)
[00:34:28 -389478.409511] AUTODETECT spr round 2 (radius: 10)
[00:35:19 -286166.808271] AUTODETECT spr round 3 (radius: 15)
[00:36:18 -241541.483720] AUTODETECT spr round 4 (radius: 20)
[00:37:32 -232179.462435] AUTODETECT spr round 5 (radius: 25)
[00:38:57 -231529.319151] SPR radius for FAST iterations: 25 (autodetect)
[00:38:57 -231529.319151] Model parameter optimization (eps = 3.000000)
[00:39:27 -230903.658644] FAST spr round 1 (radius: 25)
[00:40:35 -210231.283849] FAST spr round 2 (radius: 25)
[00:41:30 -209470.958033] FAST spr round 3 (radius: 25)
[00:42:17 -209413.665529] FAST spr round 4 (radius: 25)
[00:42:58 -209403.293279] FAST spr round 5 (radius: 25)
[00:43:35 -209403.292086] Model parameter optimization (eps = 1.000000)
[00:43:47 -209395.112223] SLOW spr round 1 (radius: 5)
[00:44:44 -209349.955863] SLOW spr round 2 (radius: 5)
[00:45:39 -209342.767359] SLOW spr round 3 (radius: 5)
[00:46:31 -209342.765023] SLOW spr round 4 (radius: 10)
[00:47:28 -209336.804036] SLOW spr round 5 (radius: 5)
[00:48:35 -209336.803177] SLOW spr round 6 (radius: 10)
[00:49:41 -209336.803027] SLOW spr round 7 (radius: 15)
[00:51:30 -209336.802903] SLOW spr round 8 (radius: 20)
[00:54:27 -209336.802780] SLOW spr round 9 (radius: 25)
[00:58:00 -209336.802656] Model parameter optimization (eps = 0.100000)

[00:58:09] ML tree search #2, logLikelihood: -209336.375012

[00:58:09 -713192.925804] Initial branch length optimization
[00:58:13 -574896.683467] Model parameter optimization (eps = 10.000000)
[00:58:57 -572099.149719] AUTODETECT spr round 1 (radius: 5)
[00:59:44 -376682.184493] AUTODETECT spr round 2 (radius: 10)
[01:00:37 -277386.632043] AUTODETECT spr round 3 (radius: 15)
[01:01:38 -238133.536743] AUTODETECT spr round 4 (radius: 20)
[01:02:51 -230790.666325] AUTODETECT spr round 5 (radius: 25)
[01:04:04 -229514.499696] SPR radius for FAST iterations: 25 (autodetect)
[01:04:04 -229514.499696] Model parameter optimization (eps = 3.000000)
[01:04:34 -228717.149647] FAST spr round 1 (radius: 25)
[01:05:56 -209871.800230] FAST spr round 2 (radius: 25)
[01:06:53 -209414.133955] FAST spr round 3 (radius: 25)
[01:07:43 -209385.775041] FAST spr round 4 (radius: 25)
[01:08:25 -209374.429227] FAST spr round 5 (radius: 25)
[01:09:04 -209374.188091] FAST spr round 6 (radius: 25)
[01:09:42 -209374.187364] Model parameter optimization (eps = 1.000000)
[01:09:57 -209369.120955] SLOW spr round 1 (radius: 5)
[01:10:55 -209329.192102] SLOW spr round 2 (radius: 5)
[01:11:50 -209327.711662] SLOW spr round 3 (radius: 5)
[01:12:44 -209327.710546] SLOW spr round 4 (radius: 10)
[01:13:43 -209324.832970] SLOW spr round 5 (radius: 5)
[01:14:55 -209324.832555] SLOW spr round 6 (radius: 10)
[01:16:02 -209324.832400] SLOW spr round 7 (radius: 15)
[01:17:48 -209324.832257] SLOW spr round 8 (radius: 20)
[01:20:40 -209324.410858] SLOW spr round 9 (radius: 5)
[01:21:59 -209324.406162] SLOW spr round 10 (radius: 10)
[01:23:15 -209324.405753] SLOW spr round 11 (radius: 15)
[01:25:00 -209324.405592] SLOW spr round 12 (radius: 20)
[01:27:53 -209324.405453] SLOW spr round 13 (radius: 25)
[01:31:19 -209324.405318] Model parameter optimization (eps = 0.100000)

[01:31:28] ML tree search #3, logLikelihood: -209324.111865

[01:31:28 -711024.910281] Initial branch length optimization
[01:31:31 -575908.825768] Model parameter optimization (eps = 10.000000)
[01:32:22 -573167.342145] AUTODETECT spr round 1 (radius: 5)
[01:33:07 -381420.344935] AUTODETECT spr round 2 (radius: 10)
[01:34:00 -284751.897716] AUTODETECT spr round 3 (radius: 15)
[01:35:07 -239173.855520] AUTODETECT spr round 4 (radius: 20)
[01:36:35 -228009.140429] AUTODETECT spr round 5 (radius: 25)
[01:38:26 -227930.377374] SPR radius for FAST iterations: 25 (autodetect)
[01:38:26 -227930.377374] Model parameter optimization (eps = 3.000000)
[01:39:01 -227075.387075] FAST spr round 1 (radius: 25)
[01:41:44 -209969.260420] FAST spr round 2 (radius: 25)
[01:42:39 -209419.588176] FAST spr round 3 (radius: 25)
[01:43:28 -209380.093285] FAST spr round 4 (radius: 25)
[01:44:10 -209373.010397] FAST spr round 5 (radius: 25)
[01:44:48 -209372.998355] Model parameter optimization (eps = 1.000000)
[01:44:57 -209370.880308] SLOW spr round 1 (radius: 5)
[01:45:54 -209338.717282] SLOW spr round 2 (radius: 5)
[01:46:49 -209338.342021] SLOW spr round 3 (radius: 5)
[01:47:44 -209338.341597] SLOW spr round 4 (radius: 10)
[01:48:43 -209335.449615] SLOW spr round 5 (radius: 5)
[01:49:53 -209335.448989] SLOW spr round 6 (radius: 10)
[01:50:58 -209335.448596] SLOW spr round 7 (radius: 15)
[01:52:36 -209335.448202] SLOW spr round 8 (radius: 20)
[01:55:17 -209334.488903] SLOW spr round 9 (radius: 5)
[01:56:36 -209334.487234] SLOW spr round 10 (radius: 10)
[01:57:48 -209334.486976] SLOW spr round 11 (radius: 15)
[01:59:25 -209334.486754] SLOW spr round 12 (radius: 20)
[02:02:05 -209334.486534] SLOW spr round 13 (radius: 25)
[02:05:23 -209334.486314] Model parameter optimization (eps = 0.100000)

[02:05:29] ML tree search #4, logLikelihood: -209334.404730

[02:05:29 -706622.060350] Initial branch length optimization
[02:05:32 -565283.938641] Model parameter optimization (eps = 10.000000)
[02:06:31 -562846.723375] AUTODETECT spr round 1 (radius: 5)
[02:07:16 -385280.123341] AUTODETECT spr round 2 (radius: 10)
[02:08:08 -289861.360200] AUTODETECT spr round 3 (radius: 15)
[02:09:09 -242067.345829] AUTODETECT spr round 4 (radius: 20)
[02:10:27 -228320.224419] AUTODETECT spr round 5 (radius: 25)
[02:11:59 -228001.532591] SPR radius for FAST iterations: 25 (autodetect)
[02:11:59 -228001.532591] Model parameter optimization (eps = 3.000000)
[02:12:27 -227300.469191] FAST spr round 1 (radius: 25)
[02:13:39 -210306.199429] FAST spr round 2 (radius: 25)
[02:14:37 -209482.808669] FAST spr round 3 (radius: 25)
[02:15:27 -209366.923086] FAST spr round 4 (radius: 25)
[02:16:10 -209358.278075] FAST spr round 5 (radius: 25)
[02:16:50 -209350.795125] FAST spr round 6 (radius: 25)
[02:17:27 -209350.792032] Model parameter optimization (eps = 1.000000)
[02:17:41 -209342.141447] SLOW spr round 1 (radius: 5)
[02:18:39 -209322.520514] SLOW spr round 2 (radius: 5)
[02:19:33 -209322.518759] SLOW spr round 3 (radius: 10)
[02:20:30 -209321.933105] SLOW spr round 4 (radius: 5)
[02:21:41 -209321.929572] SLOW spr round 5 (radius: 10)
[02:22:47 -209321.928753] SLOW spr round 6 (radius: 15)
[02:24:32 -209321.928489] SLOW spr round 7 (radius: 20)
[02:27:22 -209321.928403] SLOW spr round 8 (radius: 25)
[02:30:51 -209319.114104] SLOW spr round 9 (radius: 5)
[02:32:11 -209319.113888] SLOW spr round 10 (radius: 10)
[02:33:25 -209319.113879] SLOW spr round 11 (radius: 15)
[02:35:08 -209319.113876] SLOW spr round 12 (radius: 20)
[02:37:59 -209319.113875] SLOW spr round 13 (radius: 25)
[02:41:28 -209319.113873] Model parameter optimization (eps = 0.100000)

[02:41:36] ML tree search #5, logLikelihood: -209318.898459

[02:41:36 -702036.554571] Initial branch length optimization
[02:41:39 -565851.829068] Model parameter optimization (eps = 10.000000)
[02:42:35 -563201.305931] AUTODETECT spr round 1 (radius: 5)
[02:43:21 -395068.916165] AUTODETECT spr round 2 (radius: 10)
[02:44:14 -304585.552968] AUTODETECT spr round 3 (radius: 15)
[02:45:17 -257720.799350] AUTODETECT spr round 4 (radius: 20)
[02:46:25 -238797.365074] AUTODETECT spr round 5 (radius: 25)
[02:47:53 -234991.083061] SPR radius for FAST iterations: 25 (autodetect)
[02:47:53 -234991.083061] Model parameter optimization (eps = 3.000000)
[02:48:20 -234276.040976] FAST spr round 1 (radius: 25)
[02:49:30 -210683.983992] FAST spr round 2 (radius: 25)
[02:50:28 -209467.395521] FAST spr round 3 (radius: 25)
[02:51:15 -209404.985006] FAST spr round 4 (radius: 25)
[02:51:56 -209394.557803] FAST spr round 5 (radius: 25)
[02:52:34 -209394.557085] Model parameter optimization (eps = 1.000000)
[02:52:50 -209380.782777] SLOW spr round 1 (radius: 5)
[02:53:46 -209335.696440] SLOW spr round 2 (radius: 5)
[02:54:41 -209333.211325] SLOW spr round 3 (radius: 5)
[02:55:36 -209331.831442] SLOW spr round 4 (radius: 5)
[02:56:30 -209331.830948] SLOW spr round 5 (radius: 10)
[02:57:28 -209330.434564] SLOW spr round 6 (radius: 5)
[02:58:41 -209328.893226] SLOW spr round 7 (radius: 5)
[02:59:43 -209328.863880] SLOW spr round 8 (radius: 10)
[03:00:43 -209328.862657] SLOW spr round 9 (radius: 15)
[03:02:33 -209326.042556] SLOW spr round 10 (radius: 5)
[03:03:49 -209326.042359] SLOW spr round 11 (radius: 10)
[03:05:00 -209326.042351] SLOW spr round 12 (radius: 15)
[03:06:44 -209326.042350] SLOW spr round 13 (radius: 20)
[03:09:39 -209325.949666] SLOW spr round 14 (radius: 25)
[03:13:06 -209325.933416] Model parameter optimization (eps = 0.100000)

[03:13:13] ML tree search #6, logLikelihood: -209325.669167

[03:13:13 -703782.126987] Initial branch length optimization
[03:13:17 -571297.748612] Model parameter optimization (eps = 10.000000)
[03:14:06 -568543.864620] AUTODETECT spr round 1 (radius: 5)
[03:14:52 -385746.641596] AUTODETECT spr round 2 (radius: 10)
[03:15:44 -281716.785048] AUTODETECT spr round 3 (radius: 15)
[03:16:43 -246346.914061] AUTODETECT spr round 4 (radius: 20)
[03:17:47 -234052.433880] AUTODETECT spr round 5 (radius: 25)
[03:19:06 -232193.958668] SPR radius for FAST iterations: 25 (autodetect)
[03:19:06 -232193.958668] Model parameter optimization (eps = 3.000000)
[03:19:40 -231320.343529] FAST spr round 1 (radius: 25)
[03:20:50 -210397.393783] FAST spr round 2 (radius: 25)
[03:21:42 -209495.232679] FAST spr round 3 (radius: 25)
[03:22:29 -209423.275534] FAST spr round 4 (radius: 25)
[03:23:08 -209418.026839] FAST spr round 5 (radius: 25)
[03:23:47 -209414.612715] FAST spr round 6 (radius: 25)
[03:24:27 -209403.769418] FAST spr round 7 (radius: 25)
[03:25:05 -209399.435030] FAST spr round 8 (radius: 25)
[03:25:41 -209399.434291] Model parameter optimization (eps = 1.000000)
[03:25:58 -209387.204246] SLOW spr round 1 (radius: 5)
[03:26:54 -209347.951294] SLOW spr round 2 (radius: 5)
[03:27:50 -209344.711652] SLOW spr round 3 (radius: 5)
[03:28:45 -209344.597039] SLOW spr round 4 (radius: 5)
[03:29:39 -209344.595781] SLOW spr round 5 (radius: 10)
[03:30:39 -209341.375185] SLOW spr round 6 (radius: 5)
[03:31:49 -209340.635146] SLOW spr round 7 (radius: 5)
[03:32:51 -209340.634687] SLOW spr round 8 (radius: 10)
[03:33:52 -209337.831637] SLOW spr round 9 (radius: 5)
[03:35:04 -209326.642150] SLOW spr round 10 (radius: 5)
[03:36:05 -209326.641772] SLOW spr round 11 (radius: 10)
[03:37:07 -209326.641727] SLOW spr round 12 (radius: 15)
[03:38:50 -209326.641721] SLOW spr round 13 (radius: 20)
[03:41:34 -209325.630821] SLOW spr round 14 (radius: 5)
[03:42:53 -209325.629353] SLOW spr round 15 (radius: 10)
[03:44:07 -209325.629320] SLOW spr round 16 (radius: 15)
[03:45:46 -209325.629319] SLOW spr round 17 (radius: 20)
[03:48:30 -209325.629319] SLOW spr round 18 (radius: 25)
[03:51:51 -209325.629319] Model parameter optimization (eps = 0.100000)

[03:51:59] ML tree search #7, logLikelihood: -209325.518927

[03:51:59 -698981.640499] Initial branch length optimization
[03:52:02 -567202.889623] Model parameter optimization (eps = 10.000000)
[03:53:08 -564857.989379] AUTODETECT spr round 1 (radius: 5)
[03:53:53 -389245.795032] AUTODETECT spr round 2 (radius: 10)
[03:54:46 -290081.391765] AUTODETECT spr round 3 (radius: 15)
[03:55:44 -248963.879579] AUTODETECT spr round 4 (radius: 20)
[03:56:53 -233087.122069] AUTODETECT spr round 5 (radius: 25)
[03:58:22 -232036.789908] SPR radius for FAST iterations: 25 (autodetect)
[03:58:22 -232036.789908] Model parameter optimization (eps = 3.000000)
[03:58:56 -231241.969389] FAST spr round 1 (radius: 25)
[04:00:05 -210243.180829] FAST spr round 2 (radius: 25)
[04:01:00 -209452.855582] FAST spr round 3 (radius: 25)
[04:01:47 -209400.756147] FAST spr round 4 (radius: 25)
[04:02:29 -209381.928844] FAST spr round 5 (radius: 25)
[04:03:07 -209381.917240] Model parameter optimization (eps = 1.000000)
[04:03:22 -209373.845907] SLOW spr round 1 (radius: 5)
[04:04:17 -209328.779387] SLOW spr round 2 (radius: 5)
[04:05:15 -209324.317901] SLOW spr round 3 (radius: 5)
[04:06:09 -209324.281258] SLOW spr round 4 (radius: 10)
[04:07:07 -209323.105883] SLOW spr round 5 (radius: 5)
[04:08:18 -209322.747713] SLOW spr round 6 (radius: 5)
[04:09:20 -209322.747242] SLOW spr round 7 (radius: 10)
[04:10:20 -209322.249819] SLOW spr round 8 (radius: 5)
[04:11:30 -209322.166813] SLOW spr round 9 (radius: 10)
[04:12:35 -209322.164185] SLOW spr round 10 (radius: 15)
[04:14:16 -209319.333847] SLOW spr round 11 (radius: 5)
[04:15:32 -209319.333162] SLOW spr round 12 (radius: 10)
[04:16:42 -209319.332945] SLOW spr round 13 (radius: 15)
[04:18:22 -209319.332786] SLOW spr round 14 (radius: 20)
[04:21:04 -209319.332644] SLOW spr round 15 (radius: 25)
[04:24:22 -209319.332507] Model parameter optimization (eps = 0.100000)

[04:24:26] ML tree search #8, logLikelihood: -209319.253513

[04:24:26 -706552.281216] Initial branch length optimization
[04:24:30 -573968.688733] Model parameter optimization (eps = 10.000000)
[04:25:29 -571193.351573] AUTODETECT spr round 1 (radius: 5)
[04:26:14 -374730.518611] AUTODETECT spr round 2 (radius: 10)
[04:27:05 -280523.308206] AUTODETECT spr round 3 (radius: 15)
[04:28:06 -247010.422619] AUTODETECT spr round 4 (radius: 20)
[04:29:20 -234180.567707] AUTODETECT spr round 5 (radius: 25)
[04:30:48 -234120.708772] SPR radius for FAST iterations: 25 (autodetect)
[04:30:48 -234120.708772] Model parameter optimization (eps = 3.000000)
[04:31:21 -233250.682715] FAST spr round 1 (radius: 25)
[04:32:39 -210294.232037] FAST spr round 2 (radius: 25)
[04:33:38 -209493.966823] FAST spr round 3 (radius: 25)
[04:34:27 -209404.114857] FAST spr round 4 (radius: 25)
[04:35:10 -209390.798841] FAST spr round 5 (radius: 25)
[04:35:48 -209390.798012] Model parameter optimization (eps = 1.000000)
[04:35:59 -209387.972995] SLOW spr round 1 (radius: 5)
[04:36:56 -209345.980609] SLOW spr round 2 (radius: 5)
[04:37:50 -209345.978057] SLOW spr round 3 (radius: 10)
[04:38:49 -209340.227434] SLOW spr round 4 (radius: 5)
[04:40:03 -209330.393876] SLOW spr round 5 (radius: 5)
[04:41:05 -209327.788749] SLOW spr round 6 (radius: 5)
[04:42:03 -209327.788237] SLOW spr round 7 (radius: 10)
[04:43:02 -209327.788081] SLOW spr round 8 (radius: 15)
[04:44:51 -209327.787946] SLOW spr round 9 (radius: 20)
[04:47:40 -209327.628509] SLOW spr round 10 (radius: 5)
[04:48:58 -209327.601591] SLOW spr round 11 (radius: 10)
[04:50:12 -209327.599543] SLOW spr round 12 (radius: 15)
[04:51:56 -209327.598684] SLOW spr round 13 (radius: 20)
[04:54:48 -209327.598265] SLOW spr round 14 (radius: 25)
[04:58:11 -209327.598018] Model parameter optimization (eps = 0.100000)

[04:58:17] ML tree search #9, logLikelihood: -209327.480641

[04:58:17 -710342.000875] Initial branch length optimization
[04:58:20 -570735.180275] Model parameter optimization (eps = 10.000000)
[04:59:18 -568160.386441] AUTODETECT spr round 1 (radius: 5)
[05:00:04 -402417.510859] AUTODETECT spr round 2 (radius: 10)
[05:00:58 -285980.912254] AUTODETECT spr round 3 (radius: 15)
[05:02:00 -250365.882252] AUTODETECT spr round 4 (radius: 20)
[05:03:13 -234417.063743] AUTODETECT spr round 5 (radius: 25)
[05:04:35 -233914.296320] SPR radius for FAST iterations: 25 (autodetect)
[05:04:35 -233914.296320] Model parameter optimization (eps = 3.000000)
[05:05:07 -232872.073778] FAST spr round 1 (radius: 25)
[05:06:24 -211072.832740] FAST spr round 2 (radius: 25)
[05:07:20 -209442.325530] FAST spr round 3 (radius: 25)
[05:08:08 -209380.698783] FAST spr round 4 (radius: 25)
[05:08:52 -209362.055484] FAST spr round 5 (radius: 25)
[05:09:31 -209356.587365] FAST spr round 6 (radius: 25)
[05:10:09 -209354.808192] FAST spr round 7 (radius: 25)
[05:10:46 -209354.807388] Model parameter optimization (eps = 1.000000)
[05:11:01 -209344.587925] SLOW spr round 1 (radius: 5)
[05:12:01 -209325.425037] SLOW spr round 2 (radius: 5)
[05:12:56 -209324.277326] SLOW spr round 3 (radius: 5)
[05:13:50 -209324.277280] SLOW spr round 4 (radius: 10)
[05:14:48 -209323.184087] SLOW spr round 5 (radius: 5)
[05:16:00 -209322.837559] SLOW spr round 6 (radius: 5)
[05:17:02 -209322.837530] SLOW spr round 7 (radius: 10)
[05:18:03 -209322.837525] SLOW spr round 8 (radius: 15)
[05:19:45 -209322.837521] SLOW spr round 9 (radius: 20)
[05:22:27 -209321.983069] SLOW spr round 10 (radius: 5)
[05:23:46 -209321.980622] SLOW spr round 11 (radius: 10)
[05:25:00 -209321.980525] SLOW spr round 12 (radius: 15)
[05:26:39 -209321.980513] SLOW spr round 13 (radius: 20)
[05:29:22 -209321.980509] SLOW spr round 14 (radius: 25)
[05:32:43 -209321.980507] Model parameter optimization (eps = 0.100000)

[05:32:47] ML tree search #10, logLikelihood: -209321.945313

[05:32:47 -700782.826084] Initial branch length optimization
[05:32:50 -569617.696766] Model parameter optimization (eps = 10.000000)
[05:33:44 -566821.343366] AUTODETECT spr round 1 (radius: 5)
[05:34:29 -386027.098357] AUTODETECT spr round 2 (radius: 10)
[05:35:22 -282589.458284] AUTODETECT spr round 3 (radius: 15)
[05:36:22 -246481.983272] AUTODETECT spr round 4 (radius: 20)
[05:37:37 -236321.516488] AUTODETECT spr round 5 (radius: 25)
[05:39:05 -233534.472227] SPR radius for FAST iterations: 25 (autodetect)
[05:39:05 -233534.472227] Model parameter optimization (eps = 3.000000)
[05:39:32 -232936.029846] FAST spr round 1 (radius: 25)
[05:40:45 -210337.722572] FAST spr round 2 (radius: 25)
[05:41:44 -209466.345729] FAST spr round 3 (radius: 25)
[05:42:36 -209397.689087] FAST spr round 4 (radius: 25)
[05:43:16 -209387.274464] FAST spr round 5 (radius: 25)
[05:43:54 -209387.272998] Model parameter optimization (eps = 1.000000)
[05:44:07 -209381.896163] SLOW spr round 1 (radius: 5)
[05:45:05 -209334.243992] SLOW spr round 2 (radius: 5)
[05:46:00 -209331.917898] SLOW spr round 3 (radius: 5)
[05:46:54 -209331.915073] SLOW spr round 4 (radius: 10)
[05:47:53 -209328.434118] SLOW spr round 5 (radius: 5)
[05:49:06 -209318.548663] SLOW spr round 6 (radius: 5)
[05:50:08 -209318.546233] SLOW spr round 7 (radius: 10)
[05:51:09 -209318.545812] SLOW spr round 8 (radius: 15)
[05:52:56 -209315.675627] SLOW spr round 9 (radius: 5)
[05:54:12 -209315.675294] SLOW spr round 10 (radius: 10)
[05:55:23 -209315.675148] SLOW spr round 11 (radius: 15)
[05:57:05 -209315.675009] SLOW spr round 12 (radius: 20)
[05:59:57 -209315.522164] SLOW spr round 13 (radius: 5)
[06:01:15 -209315.520177] SLOW spr round 14 (radius: 10)
[06:02:29 -209315.519991] SLOW spr round 15 (radius: 15)
[06:04:12 -209315.519852] SLOW spr round 16 (radius: 20)
[06:07:02 -209315.478192] SLOW spr round 17 (radius: 25)
[06:10:28 -209315.467472] Model parameter optimization (eps = 0.100000)

[06:10:38] ML tree search #11, logLikelihood: -209314.460412

[06:10:38 -703847.064552] Initial branch length optimization
[06:10:42 -568966.502225] Model parameter optimization (eps = 10.000000)
[06:11:44 -566154.627856] AUTODETECT spr round 1 (radius: 5)
[06:12:29 -402112.166950] AUTODETECT spr round 2 (radius: 10)
[06:13:22 -296126.296290] AUTODETECT spr round 3 (radius: 15)
[06:14:22 -237137.707345] AUTODETECT spr round 4 (radius: 20)
[06:15:36 -229484.500693] AUTODETECT spr round 5 (radius: 25)
[06:17:11 -229163.163661] SPR radius for FAST iterations: 25 (autodetect)
[06:17:11 -229163.163661] Model parameter optimization (eps = 3.000000)
[06:17:39 -228326.347793] FAST spr round 1 (radius: 25)
[06:18:50 -209883.975896] FAST spr round 2 (radius: 25)
[06:19:49 -209463.416492] FAST spr round 3 (radius: 25)
[06:20:39 -209365.794842] FAST spr round 4 (radius: 25)
[06:21:19 -209360.558558] FAST spr round 5 (radius: 25)
[06:21:57 -209359.030269] FAST spr round 6 (radius: 25)
[06:22:35 -209359.029120] Model parameter optimization (eps = 1.000000)
[06:22:50 -209354.355410] SLOW spr round 1 (radius: 5)
[06:23:47 -209327.733811] SLOW spr round 2 (radius: 5)
[06:24:43 -209325.130450] SLOW spr round 3 (radius: 5)
[06:25:37 -209322.288667] SLOW spr round 4 (radius: 5)
[06:26:31 -209322.288544] SLOW spr round 5 (radius: 10)
[06:27:28 -209322.288521] SLOW spr round 6 (radius: 15)
[06:29:20 -209322.288511] SLOW spr round 7 (radius: 20)
[06:32:11 -209321.122995] SLOW spr round 8 (radius: 5)
[06:33:30 -209321.042404] SLOW spr round 9 (radius: 10)
[06:34:45 -209321.041571] SLOW spr round 10 (radius: 15)
[06:36:30 -209318.221971] SLOW spr round 11 (radius: 5)
[06:37:45 -209318.221736] SLOW spr round 12 (radius: 10)
[06:38:57 -209318.221733] SLOW spr round 13 (radius: 15)
[06:40:41 -209318.221733] SLOW spr round 14 (radius: 20)
[06:43:34 -209318.179363] SLOW spr round 15 (radius: 25)
[06:47:03 -209318.169009] Model parameter optimization (eps = 0.100000)

[06:47:11] ML tree search #12, logLikelihood: -209318.047121

[06:47:11 -709970.695039] Initial branch length optimization
[06:47:14 -571462.302321] Model parameter optimization (eps = 10.000000)
[06:48:26 -569158.370309] AUTODETECT spr round 1 (radius: 5)
[06:49:12 -386468.422961] AUTODETECT spr round 2 (radius: 10)
[06:50:05 -287127.594108] AUTODETECT spr round 3 (radius: 15)
[06:51:03 -245714.601399] AUTODETECT spr round 4 (radius: 20)
[06:52:17 -232396.074141] AUTODETECT spr round 5 (radius: 25)
[06:53:43 -230963.061783] SPR radius for FAST iterations: 25 (autodetect)
[06:53:43 -230963.061783] Model parameter optimization (eps = 3.000000)
[06:54:15 -230058.963909] FAST spr round 1 (radius: 25)
[06:55:29 -210458.616983] FAST spr round 2 (radius: 25)
[06:56:30 -209616.808289] FAST spr round 3 (radius: 25)
[06:57:19 -209385.274125] FAST spr round 4 (radius: 25)
[06:58:00 -209381.963332] FAST spr round 5 (radius: 25)
[06:58:38 -209381.951628] Model parameter optimization (eps = 1.000000)
[06:58:52 -209376.155784] SLOW spr round 1 (radius: 5)
[06:59:48 -209347.425419] SLOW spr round 2 (radius: 5)
[07:00:43 -209343.893773] SLOW spr round 3 (radius: 5)
[07:01:38 -209341.439619] SLOW spr round 4 (radius: 5)
[07:02:32 -209341.439566] SLOW spr round 5 (radius: 10)
[07:03:31 -209338.205280] SLOW spr round 6 (radius: 5)
[07:04:42 -209337.465135] SLOW spr round 7 (radius: 5)
[07:05:44 -209337.465106] SLOW spr round 8 (radius: 10)
[07:06:46 -209337.465106] SLOW spr round 9 (radius: 15)
[07:08:33 -209337.465106] SLOW spr round 10 (radius: 20)
[07:11:26 -209337.268056] SLOW spr round 11 (radius: 5)
[07:12:45 -209337.266422] SLOW spr round 12 (radius: 10)
[07:14:00 -209337.266379] SLOW spr round 13 (radius: 15)
[07:15:42 -209337.266376] SLOW spr round 14 (radius: 20)
[07:18:35 -209337.221768] SLOW spr round 15 (radius: 25)
[07:22:03 -209337.211302] Model parameter optimization (eps = 0.100000)

[07:22:11] ML tree search #13, logLikelihood: -209336.924211

[07:22:11 -706313.841090] Initial branch length optimization
[07:22:15 -574131.467763] Model parameter optimization (eps = 10.000000)
[07:23:10 -570921.543946] AUTODETECT spr round 1 (radius: 5)
[07:23:55 -397688.757076] AUTODETECT spr round 2 (radius: 10)
[07:24:48 -297410.903009] AUTODETECT spr round 3 (radius: 15)
[07:25:51 -242434.770787] AUTODETECT spr round 4 (radius: 20)
[07:27:02 -233152.856640] AUTODETECT spr round 5 (radius: 25)
[07:28:25 -233057.494550] SPR radius for FAST iterations: 25 (autodetect)
[07:28:25 -233057.494550] Model parameter optimization (eps = 3.000000)
[07:28:57 -232203.567568] FAST spr round 1 (radius: 25)
[07:30:10 -210768.468730] FAST spr round 2 (radius: 25)
[07:31:11 -209596.364849] FAST spr round 3 (radius: 25)
[07:32:00 -209459.627220] FAST spr round 4 (radius: 25)
[07:32:42 -209396.379073] FAST spr round 5 (radius: 25)
[07:33:20 -209395.546940] FAST spr round 6 (radius: 25)
[07:33:56 -209395.546599] Model parameter optimization (eps = 1.000000)
[07:34:09 -209392.430990] SLOW spr round 1 (radius: 5)
[07:35:05 -209369.570101] SLOW spr round 2 (radius: 5)
[07:36:01 -209368.220030] SLOW spr round 3 (radius: 5)
[07:36:57 -209364.402069] SLOW spr round 4 (radius: 5)
[07:37:52 -209361.305728] SLOW spr round 5 (radius: 5)
[07:38:52 -209349.393974] SLOW spr round 6 (radius: 5)
[07:39:47 -209347.506169] SLOW spr round 7 (radius: 5)
[07:40:41 -209347.503322] SLOW spr round 8 (radius: 10)
[07:41:39 -209341.852854] SLOW spr round 9 (radius: 5)
[07:42:51 -209341.846952] SLOW spr round 10 (radius: 10)
[07:43:53 -209341.846572] SLOW spr round 11 (radius: 15)
[07:45:29 -209338.365667] SLOW spr round 12 (radius: 5)
[07:46:46 -209336.683856] SLOW spr round 13 (radius: 5)
[07:47:51 -209336.681948] SLOW spr round 14 (radius: 10)
[07:48:52 -209336.680921] SLOW spr round 15 (radius: 15)
[07:50:37 -209336.680208] SLOW spr round 16 (radius: 20)
[07:53:23 -209333.795487] SLOW spr round 17 (radius: 5)
[07:54:42 -209333.790541] SLOW spr round 18 (radius: 10)
[07:55:54 -209333.790219] SLOW spr round 19 (radius: 15)
[07:57:35 -209333.790076] SLOW spr round 20 (radius: 20)
[08:00:19 -209333.789971] SLOW spr round 21 (radius: 25)
[08:03:35 -209333.789892] Model parameter optimization (eps = 0.100000)

[08:03:40] ML tree search #14, logLikelihood: -209333.702416

[08:03:40 -713838.571994] Initial branch length optimization
[08:03:43 -575591.973474] Model parameter optimization (eps = 10.000000)
[08:04:43 -573169.532680] AUTODETECT spr round 1 (radius: 5)
[08:05:28 -395442.903957] AUTODETECT spr round 2 (radius: 10)
[08:06:21 -292739.174882] AUTODETECT spr round 3 (radius: 15)
[08:07:22 -258680.173624] AUTODETECT spr round 4 (radius: 20)
[08:08:36 -245615.945741] AUTODETECT spr round 5 (radius: 25)
[08:11:11 -236585.651384] SPR radius for FAST iterations: 25 (autodetect)
[08:11:11 -236585.651384] Model parameter optimization (eps = 3.000000)
[08:11:45 -235703.813250] FAST spr round 1 (radius: 25)
[08:13:01 -210196.699920] FAST spr round 2 (radius: 25)
[08:13:55 -209506.886440] FAST spr round 3 (radius: 25)
[08:14:44 -209406.384043] FAST spr round 4 (radius: 25)
[08:15:26 -209387.868943] FAST spr round 5 (radius: 25)
[08:16:05 -209387.864920] Model parameter optimization (eps = 1.000000)
[08:16:23 -209368.170299] SLOW spr round 1 (radius: 5)
[08:17:22 -209337.614977] SLOW spr round 2 (radius: 5)
[08:18:15 -209336.400573] SLOW spr round 3 (radius: 5)
[08:19:08 -209336.398898] SLOW spr round 4 (radius: 10)
[08:20:06 -209332.919605] SLOW spr round 5 (radius: 5)
[08:21:17 -209332.915941] SLOW spr round 6 (radius: 10)
[08:22:22 -209332.914986] SLOW spr round 7 (radius: 15)
[08:24:01 -209332.914585] SLOW spr round 8 (radius: 20)
[08:26:47 -209332.621936] SLOW spr round 9 (radius: 5)
[08:28:05 -209332.620316] SLOW spr round 10 (radius: 10)
[08:29:19 -209332.620136] SLOW spr round 11 (radius: 15)
[08:30:57 -209332.619991] SLOW spr round 12 (radius: 20)
[08:33:38 -209332.619851] SLOW spr round 13 (radius: 25)
[08:36:55 -209332.619831] Model parameter optimization (eps = 0.100000)

[08:37:03] ML tree search #15, logLikelihood: -209332.242214

[08:37:03 -702509.608708] Initial branch length optimization
[08:37:06 -564671.216508] Model parameter optimization (eps = 10.000000)
[08:37:54 -561907.637909] AUTODETECT spr round 1 (radius: 5)
[08:38:38 -389058.043565] AUTODETECT spr round 2 (radius: 10)
[08:39:30 -298745.246813] AUTODETECT spr round 3 (radius: 15)
[08:40:32 -239362.200052] AUTODETECT spr round 4 (radius: 20)
[08:41:45 -229134.828670] AUTODETECT spr round 5 (radius: 25)
[08:43:06 -228168.673589] SPR radius for FAST iterations: 25 (autodetect)
[08:43:06 -228168.673589] Model parameter optimization (eps = 3.000000)
[08:43:32 -227448.981719] FAST spr round 1 (radius: 25)
[08:44:46 -210260.598223] FAST spr round 2 (radius: 25)
[08:45:44 -209605.034081] FAST spr round 3 (radius: 25)
[08:46:35 -209382.114749] FAST spr round 4 (radius: 25)
[08:47:14 -209379.928943] FAST spr round 5 (radius: 25)
[08:47:51 -209379.926794] Model parameter optimization (eps = 1.000000)
[08:48:05 -209370.797478] SLOW spr round 1 (radius: 5)
[08:49:04 -209332.637024] SLOW spr round 2 (radius: 5)
[08:49:59 -209330.697887] SLOW spr round 3 (radius: 5)
[08:50:53 -209330.696031] SLOW spr round 4 (radius: 10)
[08:52:39 -209327.238239] SLOW spr round 5 (radius: 5)
[08:54:57 -209327.236679] SLOW spr round 6 (radius: 10)
[08:57:07 -209327.236447] SLOW spr round 7 (radius: 15)
[09:00:38 -209324.546339] SLOW spr round 8 (radius: 5)
[09:03:06 -209323.309835] SLOW spr round 9 (radius: 5)
[09:04:10 -209323.309225] SLOW spr round 10 (radius: 10)
[09:05:13 -209323.309008] SLOW spr round 11 (radius: 15)
[09:07:00 -209323.308842] SLOW spr round 12 (radius: 20)
[09:09:49 -209323.308692] SLOW spr round 13 (radius: 25)
[09:13:17 -209323.308547] Model parameter optimization (eps = 0.100000)

[09:13:26] ML tree search #16, logLikelihood: -209322.978218

[09:13:26 -699346.447901] Initial branch length optimization
[09:13:29 -564108.701923] Model parameter optimization (eps = 10.000000)
[09:14:31 -561839.041484] AUTODETECT spr round 1 (radius: 5)
[09:15:16 -380031.037852] AUTODETECT spr round 2 (radius: 10)
[09:16:08 -293633.426333] AUTODETECT spr round 3 (radius: 15)
[09:17:07 -259507.819202] AUTODETECT spr round 4 (radius: 20)
[09:18:24 -241454.414726] AUTODETECT spr round 5 (radius: 25)
[09:19:58 -234478.877123] SPR radius for FAST iterations: 25 (autodetect)
[09:19:58 -234478.877123] Model parameter optimization (eps = 3.000000)
[09:20:26 -233759.791219] FAST spr round 1 (radius: 25)
[09:21:43 -210198.821219] FAST spr round 2 (radius: 25)
[09:22:41 -209447.544160] FAST spr round 3 (radius: 25)
[09:23:30 -209407.282019] FAST spr round 4 (radius: 25)
[09:24:11 -209400.854897] FAST spr round 5 (radius: 25)
[09:24:49 -209400.853908] Model parameter optimization (eps = 1.000000)
[09:25:05 -209388.325493] SLOW spr round 1 (radius: 5)
[09:26:03 -209342.596064] SLOW spr round 2 (radius: 5)
[09:27:00 -209337.267227] SLOW spr round 3 (radius: 5)
[09:27:54 -209337.266438] SLOW spr round 4 (radius: 10)
[09:28:54 -209333.983802] SLOW spr round 5 (radius: 5)
[09:30:06 -209333.242181] SLOW spr round 6 (radius: 5)
[09:31:07 -209333.241482] SLOW spr round 7 (radius: 10)
[09:32:09 -209333.241198] SLOW spr round 8 (radius: 15)
[09:33:58 -209333.240983] SLOW spr round 9 (radius: 20)
[09:36:48 -209332.947436] SLOW spr round 10 (radius: 5)
[09:38:09 -209331.871670] SLOW spr round 11 (radius: 5)
[09:39:16 -209331.843330] SLOW spr round 12 (radius: 10)
[09:40:20 -209331.839943] SLOW spr round 13 (radius: 15)
[09:42:10 -209331.837302] SLOW spr round 14 (radius: 20)
[09:45:02 -209331.835233] SLOW spr round 15 (radius: 25)
[09:48:26 -209331.833603] Model parameter optimization (eps = 0.100000)

[09:48:36] ML tree search #17, logLikelihood: -209331.171104

[09:48:36 -700644.517257] Initial branch length optimization
[09:48:39 -567443.199115] Model parameter optimization (eps = 10.000000)
[09:49:32 -564568.350293] AUTODETECT spr round 1 (radius: 5)
[09:50:17 -398666.899059] AUTODETECT spr round 2 (radius: 10)
[09:51:10 -289115.757746] AUTODETECT spr round 3 (radius: 15)
[09:52:09 -245195.723858] AUTODETECT spr round 4 (radius: 20)
[09:53:17 -231424.229794] AUTODETECT spr round 5 (radius: 25)
[09:54:45 -229907.114821] SPR radius for FAST iterations: 25 (autodetect)
[09:54:45 -229907.114821] Model parameter optimization (eps = 3.000000)
[09:55:13 -229064.889147] FAST spr round 1 (radius: 25)
[09:56:18 -209963.757173] FAST spr round 2 (radius: 25)
[09:57:09 -209398.790681] FAST spr round 3 (radius: 25)
[09:57:55 -209375.342772] FAST spr round 4 (radius: 25)
[09:58:36 -209364.700227] FAST spr round 5 (radius: 25)
[09:59:14 -209363.189056] FAST spr round 6 (radius: 25)
[09:59:50 -209363.186268] Model parameter optimization (eps = 1.000000)
[10:00:00 -209360.546471] SLOW spr round 1 (radius: 5)
[10:00:56 -209330.881861] SLOW spr round 2 (radius: 5)
[10:01:53 -209326.270372] SLOW spr round 3 (radius: 5)
[10:02:47 -209326.268760] SLOW spr round 4 (radius: 10)
[10:03:45 -209326.268562] SLOW spr round 5 (radius: 15)
[10:05:39 -209323.411664] SLOW spr round 6 (radius: 5)
[10:06:55 -209323.411472] SLOW spr round 7 (radius: 10)
[10:08:07 -209323.411466] SLOW spr round 8 (radius: 15)
[10:09:53 -209323.411465] SLOW spr round 9 (radius: 20)
[10:12:47 -209323.256082] SLOW spr round 10 (radius: 5)
[10:14:08 -209322.949667] SLOW spr round 11 (radius: 5)
[10:15:14 -209322.946205] SLOW spr round 12 (radius: 10)
[10:16:18 -209322.945096] SLOW spr round 13 (radius: 15)
[10:18:07 -209322.944627] SLOW spr round 14 (radius: 20)
[10:21:01 -209322.944428] SLOW spr round 15 (radius: 25)
[10:24:30 -209322.944338] Model parameter optimization (eps = 0.100000)

[10:24:39] ML tree search #18, logLikelihood: -209322.561067

[10:24:39 -704070.185991] Initial branch length optimization
[10:24:42 -568968.763428] Model parameter optimization (eps = 10.000000)
[10:25:45 -566573.388784] AUTODETECT spr round 1 (radius: 5)
[10:26:30 -380361.023472] AUTODETECT spr round 2 (radius: 10)
[10:27:23 -287969.396658] AUTODETECT spr round 3 (radius: 15)
[10:28:22 -250514.858905] AUTODETECT spr round 4 (radius: 20)
[10:29:39 -234076.723836] AUTODETECT spr round 5 (radius: 25)
[10:31:14 -233730.149140] SPR radius for FAST iterations: 25 (autodetect)
[10:31:14 -233730.149140] Model parameter optimization (eps = 3.000000)
[10:31:46 -232985.921373] FAST spr round 1 (radius: 25)
[10:33:01 -209966.078235] FAST spr round 2 (radius: 25)
[10:33:57 -209429.213317] FAST spr round 3 (radius: 25)
[10:34:46 -209389.463114] FAST spr round 4 (radius: 25)
[10:35:29 -209383.473488] FAST spr round 5 (radius: 25)
[10:36:07 -209383.472871] Model parameter optimization (eps = 1.000000)
[10:36:18 -209379.595186] SLOW spr round 1 (radius: 5)
[10:37:16 -209350.167045] SLOW spr round 2 (radius: 5)
[10:38:10 -209350.166145] SLOW spr round 3 (radius: 10)
[10:39:09 -209347.621527] SLOW spr round 4 (radius: 5)
[10:40:23 -209339.302566] SLOW spr round 5 (radius: 5)
[10:41:29 -209336.236198] SLOW spr round 6 (radius: 5)
[10:42:28 -209336.128017] SLOW spr round 7 (radius: 5)
[10:43:24 -209336.125511] SLOW spr round 8 (radius: 10)
[10:44:22 -209335.227483] SLOW spr round 9 (radius: 5)
[10:45:33 -209335.227143] SLOW spr round 10 (radius: 10)
[10:46:37 -209335.227099] SLOW spr round 11 (radius: 15)
[10:48:16 -209335.227088] SLOW spr round 12 (radius: 20)
[10:50:58 -209332.285739] SLOW spr round 13 (radius: 5)
[10:52:16 -209332.284702] SLOW spr round 14 (radius: 10)
[10:53:29 -209332.284671] SLOW spr round 15 (radius: 15)
[10:55:06 -209332.284669] SLOW spr round 16 (radius: 20)
[10:57:47 -209332.284669] SLOW spr round 17 (radius: 25)
[11:01:07 -209332.284669] Model parameter optimization (eps = 0.100000)

[11:01:10] ML tree search #19, logLikelihood: -209332.249226

[11:01:10 -701323.031437] Initial branch length optimization
[11:01:13 -566444.039352] Model parameter optimization (eps = 10.000000)
[11:02:08 -564139.155839] AUTODETECT spr round 1 (radius: 5)
[11:02:54 -381028.570464] AUTODETECT spr round 2 (radius: 10)
[11:03:46 -282699.584069] AUTODETECT spr round 3 (radius: 15)
[11:04:47 -238320.820032] AUTODETECT spr round 4 (radius: 20)
[11:06:00 -232868.359524] AUTODETECT spr round 5 (radius: 25)
[11:07:19 -231835.430893] SPR radius for FAST iterations: 25 (autodetect)
[11:07:19 -231835.430893] Model parameter optimization (eps = 3.000000)
[11:07:52 -230951.465166] FAST spr round 1 (radius: 25)
[11:08:59 -210424.881885] FAST spr round 2 (radius: 25)
[11:09:54 -209425.442733] FAST spr round 3 (radius: 25)
[11:10:44 -209378.207298] FAST spr round 4 (radius: 25)
[11:11:24 -209368.075733] FAST spr round 5 (radius: 25)
[11:12:02 -209367.263547] FAST spr round 6 (radius: 25)
[11:12:39 -209367.263047] Model parameter optimization (eps = 1.000000)
[11:12:53 -209362.926940] SLOW spr round 1 (radius: 5)
[11:13:50 -209322.751831] SLOW spr round 2 (radius: 5)
[11:14:44 -209322.104280] SLOW spr round 3 (radius: 5)
[11:15:38 -209322.103272] SLOW spr round 4 (radius: 10)
[11:16:36 -209321.510367] SLOW spr round 5 (radius: 5)
[11:17:49 -209319.808885] SLOW spr round 6 (radius: 5)
[11:18:51 -209319.808832] SLOW spr round 7 (radius: 10)
[11:19:51 -209318.548021] SLOW spr round 8 (radius: 5)
[11:21:02 -209318.547039] SLOW spr round 9 (radius: 10)
[11:22:07 -209318.546976] SLOW spr round 10 (radius: 15)
[11:23:51 -209318.546970] SLOW spr round 11 (radius: 20)
[11:26:44 -209314.689465] SLOW spr round 12 (radius: 5)
[11:28:03 -209314.684127] SLOW spr round 13 (radius: 10)
[11:29:16 -209314.683763] SLOW spr round 14 (radius: 15)
[11:30:58 -209314.683725] SLOW spr round 15 (radius: 20)
[11:33:49 -209314.643296] SLOW spr round 16 (radius: 25)
[11:37:14 -209314.633023] Model parameter optimization (eps = 0.100000)

[11:37:25] ML tree search #20, logLikelihood: -209314.043143


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.168995,0.449103) (0.088942,1.159946) (0.393051,0.608474) (0.349012,1.666918) 
   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: -209314.043143

AIC score: 420762.086286 / AICc score: 437158.575494 / BIC score: 426199.404353
Free parameters (model + branch lengths): 1067

WARNING: Best ML tree contains 1 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UL68/3_mltree/Q9UL68.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UL68/3_mltree/Q9UL68.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UL68/3_mltree/Q9UL68.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UL68/3_mltree/Q9UL68.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UL68/3_mltree/Q9UL68.raxml.log

Analysis started: 14-Jul-2021 15:18:34 / finished: 15-Jul-2021 02:56:00

Elapsed time: 41845.143 seconds

Consumed energy: 3915.923 Wh (= 20 km in an electric car, or 98 km with an e-scooter!)