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 13-Jul-2021 22:14:45 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P21817/2_msa/P21817_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P21817/3_mltree/P21817 --seed 2 --threads 10 --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 (10 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P21817/2_msa/P21817_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 5398 sites

WARNING: Sequences tr_A0A091F8R5_A0A091F8R5_CORBR_85066 and tr_A0A091GEB7_A0A091GEB7_9AVES_55661 are exactly identical!
WARNING: Sequences tr_A0A1I7T9I4_A0A1I7T9I4_9PELO_1561998 and tr_A0A1I7T9I5_A0A1I7T9I5_9PELO_1561998 are exactly identical!
WARNING: Sequences tr_A0A1I7T9I6_A0A1I7T9I6_9PELO_1561998 and tr_A0A1I7T9I7_A0A1I7T9I7_9PELO_1561998 are exactly identical!
WARNING: Sequences tr_A0A1D1VKJ5_A0A1D1VKJ5_RAMVA_947166 and tr_A0A1D1VMT0_A0A1D1VMT0_RAMVA_947166 are exactly identical!
WARNING: Sequences tr_A0A2D0PYS3_A0A2D0PYS3_ICTPU_7998 and tr_A0A2D0Q040_A0A2D0Q040_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PYS3_A0A2D0PYS3_ICTPU_7998 and tr_A0A2D0Q1S8_A0A2D0Q1S8_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0PYS3_A0A2D0PYS3_ICTPU_7998 and tr_A0A2D0Q2R4_A0A2D0Q2R4_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QRX6_A0A2D0QRX6_ICTPU_7998 and tr_A0A2D0QSE3_A0A2D0QSE3_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QRX6_A0A2D0QRX6_ICTPU_7998 and tr_A0A2D0QU11_A0A2D0QU11_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QRX6_A0A2D0QRX6_ICTPU_7998 and tr_A0A2D0QUQ6_A0A2D0QUQ6_ICTPU_7998 are exactly identical!
WARNING: Duplicate sequences found: 10

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/P21817/3_mltree/P21817.raxml.reduced.phy

Alignment comprises 1 partitions and 5398 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 5398 / 5398
Gaps: 52.38 %
Invariant sites: 0.06 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P21817/3_mltree/P21817.raxml.rba

Parallelization scheme autoconfig: 1 worker(s) x 10 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 / 540 / 43200
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:01 -4244377.850439] Initial branch length optimization
[00:00:29 -3423826.425691] Model parameter optimization (eps = 10.000000)
[00:02:41 -3417324.865528] AUTODETECT spr round 1 (radius: 5)
[00:07:33 -2197230.756125] AUTODETECT spr round 2 (radius: 10)
[00:12:50 -1585165.127000] AUTODETECT spr round 3 (radius: 15)
[00:18:46 -1145724.073104] AUTODETECT spr round 4 (radius: 20)
[00:25:24 -1040320.713543] AUTODETECT spr round 5 (radius: 25)
[00:33:53 -1023779.229344] SPR radius for FAST iterations: 25 (autodetect)
[00:33:53 -1023779.229344] Model parameter optimization (eps = 3.000000)
[00:35:37 -1021158.990711] FAST spr round 1 (radius: 25)
[00:44:44 -929059.152329] FAST spr round 2 (radius: 25)
[00:51:17 -926039.211342] FAST spr round 3 (radius: 25)
[00:56:11 -925790.305204] FAST spr round 4 (radius: 25)
[01:00:15 -925777.772224] FAST spr round 5 (radius: 25)
[01:03:58 -925769.274965] FAST spr round 6 (radius: 25)
[01:07:21 -925769.209894] Model parameter optimization (eps = 1.000000)
[01:08:00 -925731.632186] SLOW spr round 1 (radius: 5)
[01:13:00 -925581.773556] SLOW spr round 2 (radius: 5)
[01:18:10 -925577.372289] SLOW spr round 3 (radius: 5)
[01:23:08 -925577.357595] SLOW spr round 4 (radius: 10)
[01:28:51 -925573.966582] SLOW spr round 5 (radius: 5)
[01:35:16 -925573.965120] SLOW spr round 6 (radius: 10)
[01:41:51 -925573.964392] SLOW spr round 7 (radius: 15)
[01:51:50 -925573.963717] SLOW spr round 8 (radius: 20)
[02:08:36 -925573.571252] SLOW spr round 9 (radius: 5)
[02:15:33 -925573.556550] SLOW spr round 10 (radius: 10)
[02:22:47 -925573.556004] SLOW spr round 11 (radius: 15)
[02:32:37 -925573.555506] SLOW spr round 12 (radius: 20)
[02:49:23 -925573.555034] SLOW spr round 13 (radius: 25)
[03:10:53 -925573.554574] Model parameter optimization (eps = 0.100000)

[03:11:17] ML tree search #1, logLikelihood: -925572.971838

[03:11:17 -4257399.961365] Initial branch length optimization
[03:11:42 -3467399.949116] Model parameter optimization (eps = 10.000000)
[03:14:03 -3460572.109986] AUTODETECT spr round 1 (radius: 5)
[03:19:08 -2155876.858685] AUTODETECT spr round 2 (radius: 10)
[03:24:36 -1438059.021256] AUTODETECT spr round 3 (radius: 15)
[03:30:34 -1183511.401989] AUTODETECT spr round 4 (radius: 20)
[03:37:16 -1065903.382752] AUTODETECT spr round 5 (radius: 25)
[03:45:34 -1028767.221825] SPR radius for FAST iterations: 25 (autodetect)
[03:45:34 -1028767.221825] Model parameter optimization (eps = 3.000000)
[03:47:10 -1026002.317187] FAST spr round 1 (radius: 25)
[03:56:42 -930464.153346] FAST spr round 2 (radius: 25)
[04:03:37 -926073.812742] FAST spr round 3 (radius: 25)
[04:08:43 -925766.194000] FAST spr round 4 (radius: 25)
[04:12:51 -925749.761443] FAST spr round 5 (radius: 25)
[04:16:29 -925749.631597] FAST spr round 6 (radius: 25)
[04:19:59 -925749.629407] Model parameter optimization (eps = 1.000000)
[04:20:41 -925724.328318] SLOW spr round 1 (radius: 5)
[04:25:54 -925613.295094] SLOW spr round 2 (radius: 5)
[04:30:58 -925612.938933] SLOW spr round 3 (radius: 5)
[04:35:52 -925612.927165] SLOW spr round 4 (radius: 10)
[04:41:25 -925609.651191] SLOW spr round 5 (radius: 5)
[04:47:54 -925609.649909] SLOW spr round 6 (radius: 10)
[04:54:29 -925609.649151] SLOW spr round 7 (radius: 15)
[05:04:33 -925609.648419] SLOW spr round 8 (radius: 20)
[05:21:32 -925609.647700] SLOW spr round 9 (radius: 25)
[05:43:09 -925608.732092] SLOW spr round 10 (radius: 5)
[05:50:17 -925608.719846] SLOW spr round 11 (radius: 10)
[05:57:45 -925608.719002] SLOW spr round 12 (radius: 15)
[06:07:42 -925601.530829] SLOW spr round 13 (radius: 5)
[06:14:30 -925601.528410] SLOW spr round 14 (radius: 10)
[06:21:30 -925601.526908] SLOW spr round 15 (radius: 15)
[06:31:24 -925601.525698] SLOW spr round 16 (radius: 20)
[06:48:31 -925601.524659] SLOW spr round 17 (radius: 25)
[07:10:19 -925601.523736] Model parameter optimization (eps = 0.100000)

[07:10:47] ML tree search #2, logLikelihood: -925600.829091

[07:10:47 -4250056.353955] Initial branch length optimization
[07:11:12 -3449228.108769] Model parameter optimization (eps = 10.000000)
[07:13:43 -3441917.227046] AUTODETECT spr round 1 (radius: 5)
[07:18:44 -2135607.594015] AUTODETECT spr round 2 (radius: 10)
[07:24:11 -1460321.374352] AUTODETECT spr round 3 (radius: 15)
[07:29:57 -1160411.776718] AUTODETECT spr round 4 (radius: 20)
[07:37:19 -1034114.878491] AUTODETECT spr round 5 (radius: 25)
[07:45:54 -1023571.834287] SPR radius for FAST iterations: 25 (autodetect)
[07:45:54 -1023571.834287] Model parameter optimization (eps = 3.000000)
[07:47:40 -1021059.981741] FAST spr round 1 (radius: 25)
[07:57:13 -929498.033460] FAST spr round 2 (radius: 25)
[08:03:57 -926017.613103] FAST spr round 3 (radius: 25)
[08:09:01 -925824.910824] FAST spr round 4 (radius: 25)
[08:13:09 -925795.228413] FAST spr round 5 (radius: 25)
[08:16:41 -925794.803470] FAST spr round 6 (radius: 25)
[08:20:06 -925794.554640] FAST spr round 7 (radius: 25)
[08:23:30 -925794.425873] FAST spr round 8 (radius: 25)
[08:26:56 -925794.401471] Model parameter optimization (eps = 1.000000)
[08:27:38 -925751.795615] SLOW spr round 1 (radius: 5)
[08:32:42 -925602.986420] SLOW spr round 2 (radius: 5)
[08:37:53 -925574.423296] SLOW spr round 3 (radius: 5)
[08:42:54 -925574.408662] SLOW spr round 4 (radius: 10)
[08:48:40 -925570.938958] SLOW spr round 5 (radius: 5)
[08:55:08 -925570.026941] SLOW spr round 6 (radius: 5)
[09:00:46 -925570.007601] SLOW spr round 7 (radius: 10)
[09:06:41 -925570.006431] SLOW spr round 8 (radius: 15)
[09:16:54 -925562.516452] SLOW spr round 9 (radius: 5)
[09:23:42 -925562.392131] SLOW spr round 10 (radius: 5)
[09:29:33 -925562.389795] SLOW spr round 11 (radius: 10)
[09:35:42 -925562.388118] SLOW spr round 12 (radius: 15)
[09:45:58 -925562.386855] SLOW spr round 13 (radius: 20)
[10:02:44 -925562.385856] SLOW spr round 14 (radius: 25)
[10:24:05 -925562.385027] Model parameter optimization (eps = 0.100000)

[10:24:25] ML tree search #3, logLikelihood: -925562.046229

[10:24:25 -4255266.565142] Initial branch length optimization
[10:24:53 -3448808.860173] Model parameter optimization (eps = 10.000000)
[10:26:55 -3441751.854553] AUTODETECT spr round 1 (radius: 5)
[10:31:57 -2154288.302926] AUTODETECT spr round 2 (radius: 10)
[10:37:16 -1481330.631262] AUTODETECT spr round 3 (radius: 15)
[10:42:59 -1212404.374250] AUTODETECT spr round 4 (radius: 20)
[10:49:41 -1050287.581515] AUTODETECT spr round 5 (radius: 25)
[10:57:22 -1034734.116865] SPR radius for FAST iterations: 25 (autodetect)
[10:57:22 -1034734.116865] Model parameter optimization (eps = 3.000000)
[10:58:53 -1032318.435597] FAST spr round 1 (radius: 25)
[11:07:29 -930283.377134] FAST spr round 2 (radius: 25)
[11:13:57 -925953.509720] FAST spr round 3 (radius: 25)
[11:19:19 -925828.812034] FAST spr round 4 (radius: 25)
[11:23:29 -925808.623323] FAST spr round 5 (radius: 25)
[11:27:15 -925796.956660] FAST spr round 6 (radius: 25)
[11:30:43 -925796.953535] Model parameter optimization (eps = 1.000000)
[11:31:25 -925719.601896] SLOW spr round 1 (radius: 5)
[11:36:51 -925557.296479] SLOW spr round 2 (radius: 5)
[11:41:59 -925549.502775] SLOW spr round 3 (radius: 5)
[11:46:52 -925549.501573] SLOW spr round 4 (radius: 10)
[11:52:25 -925549.500512] SLOW spr round 5 (radius: 15)
[12:03:16 -925549.156577] SLOW spr round 6 (radius: 5)
[12:10:47 -925549.127998] SLOW spr round 7 (radius: 10)
[12:18:37 -925549.126956] SLOW spr round 8 (radius: 15)
[12:29:52 -925549.125991] SLOW spr round 9 (radius: 20)
[12:49:16 -925549.076485] SLOW spr round 10 (radius: 25)
[13:14:37 -925549.075663] Model parameter optimization (eps = 0.100000)

[13:15:01] ML tree search #4, logLikelihood: -925548.679989

[13:15:01 -4206046.702815] Initial branch length optimization
[13:15:31 -3416158.322202] Model parameter optimization (eps = 10.000000)
[13:17:49 -3409419.628201] AUTODETECT spr round 1 (radius: 5)
[13:23:26 -2217586.677392] AUTODETECT spr round 2 (radius: 10)
[13:29:26 -1511798.015686] AUTODETECT spr round 3 (radius: 15)
[13:36:12 -1231230.055695] AUTODETECT spr round 4 (radius: 20)
[13:43:46 -1080906.342637] AUTODETECT spr round 5 (radius: 25)
[13:53:00 -1045901.680639] SPR radius for FAST iterations: 25 (autodetect)
[13:53:00 -1045901.680639] Model parameter optimization (eps = 3.000000)
[13:54:30 -1043499.499450] FAST spr round 1 (radius: 25)
[14:05:39 -930752.949349] FAST spr round 2 (radius: 25)
[14:13:07 -926008.828735] FAST spr round 3 (radius: 25)
[14:19:07 -925872.083215] FAST spr round 4 (radius: 25)
[14:23:21 -925870.953622] FAST spr round 5 (radius: 25)
[14:27:20 -925870.809036] FAST spr round 6 (radius: 25)
[14:31:08 -925870.792839] Model parameter optimization (eps = 1.000000)
[14:31:54 -925781.669366] SLOW spr round 1 (radius: 5)
[14:37:38 -925586.823115] SLOW spr round 2 (radius: 5)
[14:43:22 -925572.823463] SLOW spr round 3 (radius: 5)
[14:49:07 -925572.154526] SLOW spr round 4 (radius: 5)
[14:54:41 -925572.152463] SLOW spr round 5 (radius: 10)
[15:01:03 -925569.187646] SLOW spr round 6 (radius: 5)
[15:08:10 -925569.186464] SLOW spr round 7 (radius: 10)
[15:15:29 -925569.062096] SLOW spr round 8 (radius: 5)
[15:22:28 -925568.542933] SLOW spr round 9 (radius: 5)
[15:28:46 -925568.158405] SLOW spr round 10 (radius: 5)
[15:34:31 -925568.155971] SLOW spr round 11 (radius: 10)
[15:40:50 -925568.154618] SLOW spr round 12 (radius: 15)
[15:52:23 -925566.673298] SLOW spr round 13 (radius: 5)
[15:59:13 -925566.672769] SLOW spr round 14 (radius: 10)
[16:06:13 -925566.672389] SLOW spr round 15 (radius: 15)
[16:16:16 -925566.672085] SLOW spr round 16 (radius: 20)
[16:33:13 -925566.623395] SLOW spr round 17 (radius: 25)
[16:54:43 -925566.622891] Model parameter optimization (eps = 0.100000)

[16:55:05] ML tree search #5, logLikelihood: -925566.380336

[16:55:05 -4261509.809889] Initial branch length optimization
[16:55:28 -3471999.398830] Model parameter optimization (eps = 10.000000)
[16:57:44 -3465044.986448] AUTODETECT spr round 1 (radius: 5)
[17:02:42 -2123627.597283] AUTODETECT spr round 2 (radius: 10)
[17:08:10 -1482863.715229] AUTODETECT spr round 3 (radius: 15)
[17:14:01 -1193759.684478] AUTODETECT spr round 4 (radius: 20)
[17:20:32 -1062955.767012] AUTODETECT spr round 5 (radius: 25)
[17:29:10 -1041446.355248] SPR radius for FAST iterations: 25 (autodetect)
[17:29:10 -1041446.355248] Model parameter optimization (eps = 3.000000)
[17:30:37 -1039075.477073] FAST spr round 1 (radius: 25)
[17:39:34 -929142.457677] FAST spr round 2 (radius: 25)
[17:46:14 -925943.070706] FAST spr round 3 (radius: 25)
[17:51:31 -925779.552199] FAST spr round 4 (radius: 25)
[17:55:54 -925733.315415] FAST spr round 5 (radius: 25)
[17:59:32 -925733.070954] FAST spr round 6 (radius: 25)
[18:02:59 -925733.068162] Model parameter optimization (eps = 1.000000)
[18:03:41 -925689.194730] SLOW spr round 1 (radius: 5)
[18:09:01 -925585.625737] SLOW spr round 2 (radius: 5)
[18:14:10 -925580.977186] SLOW spr round 3 (radius: 5)
[18:19:12 -925580.818546] SLOW spr round 4 (radius: 5)
[18:24:11 -925580.806570] SLOW spr round 5 (radius: 10)
[18:29:49 -925579.917648] SLOW spr round 6 (radius: 5)
[18:36:28 -925579.319993] SLOW spr round 7 (radius: 5)
[18:42:34 -925579.319544] SLOW spr round 8 (radius: 10)
[18:48:53 -925579.319298] SLOW spr round 9 (radius: 15)
[19:00:31 -925578.421791] SLOW spr round 10 (radius: 5)
[19:07:51 -925578.161009] SLOW spr round 11 (radius: 5)
[19:14:08 -925578.129008] SLOW spr round 12 (radius: 10)
[19:20:44 -925578.127507] SLOW spr round 13 (radius: 15)
[19:32:01 -925578.126422] SLOW spr round 14 (radius: 20)
[19:50:53 -925578.125596] SLOW spr round 15 (radius: 25)
[20:14:03 -925578.124935] Model parameter optimization (eps = 0.100000)

[20:14:28] ML tree search #6, logLikelihood: -925577.676380

[20:14:28 -4226798.809256] Initial branch length optimization
[20:14:53 -3423559.665967] Model parameter optimization (eps = 10.000000)
[20:16:58 -3416874.671960] AUTODETECT spr round 1 (radius: 5)
[20:22:06 -2117290.946108] AUTODETECT spr round 2 (radius: 10)
[20:27:38 -1481993.952135] AUTODETECT spr round 3 (radius: 15)
[20:33:28 -1206860.859629] AUTODETECT spr round 4 (radius: 20)
[20:39:46 -1080628.019504] AUTODETECT spr round 5 (radius: 25)
[20:47:14 -1059030.457617] SPR radius for FAST iterations: 25 (autodetect)
[20:47:14 -1059030.457617] Model parameter optimization (eps = 3.000000)
[20:48:35 -1056652.154114] FAST spr round 1 (radius: 25)
[20:57:20 -929254.789080] FAST spr round 2 (radius: 25)
[21:03:58 -926092.863901] FAST spr round 3 (radius: 25)
[21:09:20 -925884.930191] FAST spr round 4 (radius: 25)
[21:13:29 -925873.502123] FAST spr round 5 (radius: 25)
[21:17:08 -925871.092940] FAST spr round 6 (radius: 25)
[21:20:35 -925871.069412] Model parameter optimization (eps = 1.000000)
[21:21:22 -925807.148845] SLOW spr round 1 (radius: 5)
[21:26:30 -925665.753043] SLOW spr round 2 (radius: 5)
[21:31:40 -925653.416277] SLOW spr round 3 (radius: 5)
[21:37:10 -925648.560074] SLOW spr round 4 (radius: 5)
[21:42:28 -925648.556443] SLOW spr round 5 (radius: 10)
[21:48:17 -925648.006570] SLOW spr round 6 (radius: 5)
[21:54:48 -925647.224445] SLOW spr round 7 (radius: 5)
[22:00:28 -925647.224000] SLOW spr round 8 (radius: 10)
[22:06:31 -925647.223608] SLOW spr round 9 (radius: 15)
[22:17:43 -925590.405536] SLOW spr round 10 (radius: 5)
[22:24:41 -925589.008427] SLOW spr round 11 (radius: 5)
[22:30:41 -925589.007301] SLOW spr round 12 (radius: 10)
[22:37:02 -925589.006603] SLOW spr round 13 (radius: 15)
[22:47:53 -925589.006068] SLOW spr round 14 (radius: 20)
[23:06:03 -925589.005623] SLOW spr round 15 (radius: 25)
[23:29:31 -925589.005223] Model parameter optimization (eps = 0.100000)

[23:29:56] ML tree search #7, logLikelihood: -925588.167986

[23:29:57 -4232055.392974] Initial branch length optimization
[23:30:21 -3429732.502843] Model parameter optimization (eps = 10.000000)
[23:32:47 -3423144.781161] AUTODETECT spr round 1 (radius: 5)
[23:37:47 -2161771.867440] AUTODETECT spr round 2 (radius: 10)
[23:43:11 -1415669.204884] AUTODETECT spr round 3 (radius: 15)
[23:49:02 -1136583.803976] AUTODETECT spr round 4 (radius: 20)
[23:56:24 -1029318.580362] AUTODETECT spr round 5 (radius: 25)
[24:06:35 -1012591.858968] SPR radius for FAST iterations: 25 (autodetect)
[24:06:35 -1012591.858968] Model parameter optimization (eps = 3.000000)
[24:08:08 -1009732.590189] FAST spr round 1 (radius: 25)
[24:18:27 -928188.347817] FAST spr round 2 (radius: 25)
[24:26:06 -925886.735460] FAST spr round 3 (radius: 25)
[24:32:16 -925808.111492] FAST spr round 4 (radius: 25)
[24:37:09 -925785.924849] FAST spr round 5 (radius: 25)
[24:41:28 -925785.424782] FAST spr round 6 (radius: 25)
[24:45:33 -925785.413210] Model parameter optimization (eps = 1.000000)
[24:46:21 -925738.288730] SLOW spr round 1 (radius: 5)
[24:52:19 -925573.088540] SLOW spr round 2 (radius: 5)
[24:58:30 -925552.209644] SLOW spr round 3 (radius: 5)
[25:04:30 -925552.197104] SLOW spr round 4 (radius: 10)
[25:11:09 -925551.762224] SLOW spr round 5 (radius: 5)
[25:18:51 -925551.274636] SLOW spr round 6 (radius: 5)
[25:25:35 -925551.262003] SLOW spr round 7 (radius: 10)
[25:32:40 -925551.261611] SLOW spr round 8 (radius: 15)
[25:45:23 -925551.261301] SLOW spr round 9 (radius: 20)
[26:05:57 -925551.261046] SLOW spr round 10 (radius: 25)
[26:32:08 -925551.260828] Model parameter optimization (eps = 0.100000)

[26:32:32] ML tree search #8, logLikelihood: -925551.024635

[26:32:32 -4230556.697355] Initial branch length optimization
[26:33:02 -3408693.978106] Model parameter optimization (eps = 10.000000)
[26:35:29 -3401804.887814] AUTODETECT spr round 1 (radius: 5)
[26:41:18 -2137742.480957] AUTODETECT spr round 2 (radius: 10)
[26:47:40 -1479503.392192] AUTODETECT spr round 3 (radius: 15)
[26:54:34 -1181343.285133] AUTODETECT spr round 4 (radius: 20)
[27:02:49 -1086328.204673] AUTODETECT spr round 5 (radius: 25)
[27:12:37 -1017034.219844] SPR radius for FAST iterations: 25 (autodetect)
[27:12:37 -1017034.219844] Model parameter optimization (eps = 3.000000)
[27:14:22 -1014667.647671] FAST spr round 1 (radius: 25)
[27:25:30 -928200.883539] FAST spr round 2 (radius: 25)
[27:34:09 -925965.489943] FAST spr round 3 (radius: 25)
[27:40:18 -925863.340023] FAST spr round 4 (radius: 25)
[27:45:10 -925845.073315] FAST spr round 5 (radius: 25)
[27:49:28 -925845.034166] Model parameter optimization (eps = 1.000000)
[27:50:16 -925786.114512] SLOW spr round 1 (radius: 5)
[27:56:28 -925588.482063] SLOW spr round 2 (radius: 5)
[28:01:50 -925574.002251] SLOW spr round 3 (radius: 5)
[28:07:00 -925573.716509] SLOW spr round 4 (radius: 5)
[28:12:01 -925573.696929] SLOW spr round 5 (radius: 10)
[28:17:39 -925568.387249] SLOW spr round 6 (radius: 5)
[28:24:01 -925568.380750] SLOW spr round 7 (radius: 10)
[28:30:30 -925568.378885] SLOW spr round 8 (radius: 15)
[28:40:34 -925568.327458] SLOW spr round 9 (radius: 20)
[28:57:32 -925568.326868] SLOW spr round 10 (radius: 25)
[29:19:10 -925551.861751] SLOW spr round 11 (radius: 5)
[29:26:16 -925551.833718] SLOW spr round 12 (radius: 10)
[29:33:40 -925551.833311] SLOW spr round 13 (radius: 15)
[29:43:43 -925551.832937] SLOW spr round 14 (radius: 20)
[30:00:52 -925551.832584] SLOW spr round 15 (radius: 25)
[30:22:34 -925551.832244] Model parameter optimization (eps = 0.100000)

[30:23:01] ML tree search #9, logLikelihood: -925550.820159

[30:23:02 -4205812.453535] Initial branch length optimization
[30:23:26 -3415271.415572] Model parameter optimization (eps = 10.000000)
[30:25:49 -3408462.076462] AUTODETECT spr round 1 (radius: 5)
[30:30:42 -2093766.895698] AUTODETECT spr round 2 (radius: 10)
[30:36:09 -1422426.153204] AUTODETECT spr round 3 (radius: 15)
[30:42:00 -1173816.519551] AUTODETECT spr round 4 (radius: 20)
[30:48:30 -1030854.517357] AUTODETECT spr round 5 (radius: 25)
[30:56:40 -1013506.214958] SPR radius for FAST iterations: 25 (autodetect)
[30:56:40 -1013506.214958] Model parameter optimization (eps = 3.000000)
[30:58:08 -1010623.580369] FAST spr round 1 (radius: 25)
[31:07:32 -929718.037756] FAST spr round 2 (radius: 25)
[31:14:15 -925869.850103] FAST spr round 3 (radius: 25)
[31:19:40 -925727.893395] FAST spr round 4 (radius: 25)
[31:23:52 -925717.584944] FAST spr round 5 (radius: 25)
[31:27:32 -925717.420562] FAST spr round 6 (radius: 25)
[31:31:03 -925717.414791] Model parameter optimization (eps = 1.000000)
[31:31:39 -925695.641118] SLOW spr round 1 (radius: 5)
[31:36:52 -925580.315022] SLOW spr round 2 (radius: 5)
[31:42:04 -925577.270733] SLOW spr round 3 (radius: 5)
[31:47:05 -925577.051851] SLOW spr round 4 (radius: 5)
[31:52:04 -925577.049999] SLOW spr round 5 (radius: 10)
[31:57:43 -925575.854652] SLOW spr round 6 (radius: 5)
[32:04:17 -925575.226413] SLOW spr round 7 (radius: 5)
[32:09:57 -925575.222872] SLOW spr round 8 (radius: 10)
[32:15:51 -925575.222145] SLOW spr round 9 (radius: 15)
[32:26:20 -925575.170195] SLOW spr round 10 (radius: 20)
[32:43:45 -925574.218014] SLOW spr round 11 (radius: 5)
[32:50:46 -925574.187444] SLOW spr round 12 (radius: 10)
[32:58:04 -925574.186541] SLOW spr round 13 (radius: 15)
[33:08:08 -925574.185746] SLOW spr round 14 (radius: 20)
[33:25:43 -925574.185000] SLOW spr round 15 (radius: 25)
[33:48:10 -925573.853040] SLOW spr round 16 (radius: 5)
[33:55:20 -925573.765105] SLOW spr round 17 (radius: 10)
[34:02:51 -925573.763622] SLOW spr round 18 (radius: 15)
[34:12:53 -925573.762637] SLOW spr round 19 (radius: 20)
[34:30:36 -925573.761875] SLOW spr round 20 (radius: 25)
[34:53:03 -925573.761212] Model parameter optimization (eps = 0.100000)

[34:53:23] ML tree search #10, logLikelihood: -925573.533581

[34:53:23 -4235020.191098] Initial branch length optimization
[34:53:55 -3428683.119554] Model parameter optimization (eps = 10.000000)
[34:56:24 -3422016.466150] AUTODETECT spr round 1 (radius: 5)
[35:01:30 -2190778.541783] AUTODETECT spr round 2 (radius: 10)
[35:06:59 -1444966.324819] AUTODETECT spr round 3 (radius: 15)
[35:12:49 -1156140.390416] AUTODETECT spr round 4 (radius: 20)
[35:19:40 -1032444.741530] AUTODETECT spr round 5 (radius: 25)
[35:27:45 -1026541.626475] SPR radius for FAST iterations: 25 (autodetect)
[35:27:45 -1026541.626475] Model parameter optimization (eps = 3.000000)
[35:29:08 -1023869.936156] FAST spr round 1 (radius: 25)
[35:38:45 -928289.705996] FAST spr round 2 (radius: 25)
[35:45:35 -925905.451790] FAST spr round 3 (radius: 25)
[35:50:56 -925779.618648] FAST spr round 4 (radius: 25)
[35:55:06 -925763.608690] FAST spr round 5 (radius: 25)
[35:58:41 -925763.090642] FAST spr round 6 (radius: 25)
[36:02:06 -925763.078956] Model parameter optimization (eps = 1.000000)
[36:02:48 -925715.766084] SLOW spr round 1 (radius: 5)
[36:07:54 -925589.743234] SLOW spr round 2 (radius: 5)
[36:13:08 -925584.860295] SLOW spr round 3 (radius: 5)
[36:18:09 -925584.807157] SLOW spr round 4 (radius: 10)
[36:23:51 -925584.513537] SLOW spr round 5 (radius: 5)
[36:30:17 -925584.512151] SLOW spr round 6 (radius: 10)
[36:36:56 -925584.511249] SLOW spr round 7 (radius: 15)
[36:47:25 -925583.208328] SLOW spr round 8 (radius: 5)
[36:54:16 -925583.193687] SLOW spr round 9 (radius: 10)
[37:01:21 -925583.192487] SLOW spr round 10 (radius: 15)
[37:11:36 -925583.134961] SLOW spr round 11 (radius: 20)
[37:29:17 -925583.128342] SLOW spr round 12 (radius: 25)
[37:51:30 -925582.009545] SLOW spr round 13 (radius: 5)
[37:58:43 -925582.007928] SLOW spr round 14 (radius: 10)
[38:06:22 -925582.007177] SLOW spr round 15 (radius: 15)
[38:16:47 -925582.006715] SLOW spr round 16 (radius: 20)
[38:34:27 -925582.006380] SLOW spr round 17 (radius: 25)
[38:56:37 -925582.006111] Model parameter optimization (eps = 0.100000)

[38:57:14] ML tree search #11, logLikelihood: -925580.495200

[38:57:14 -4286017.086848] Initial branch length optimization
[38:57:40 -3467886.566307] Model parameter optimization (eps = 10.000000)
[38:59:49 -3461222.266295] AUTODETECT spr round 1 (radius: 5)
[39:04:52 -2166396.759727] AUTODETECT spr round 2 (radius: 10)
[39:10:19 -1439761.210291] AUTODETECT spr round 3 (radius: 15)
[39:16:20 -1201828.095892] AUTODETECT spr round 4 (radius: 20)
[39:23:04 -1083618.490587] AUTODETECT spr round 5 (radius: 25)
[39:31:32 -1031185.921971] SPR radius for FAST iterations: 25 (autodetect)
[39:31:32 -1031185.921971] Model parameter optimization (eps = 3.000000)
[39:32:59 -1028541.421501] FAST spr round 1 (radius: 25)
[39:41:44 -929583.466921] FAST spr round 2 (radius: 25)
[39:48:12 -925895.692284] FAST spr round 3 (radius: 25)
[39:53:18 -925753.393014] FAST spr round 4 (radius: 25)
[39:57:30 -925750.631443] FAST spr round 5 (radius: 25)
[40:01:09 -925750.379392] FAST spr round 6 (radius: 25)
[40:04:43 -925749.800558] FAST spr round 7 (radius: 25)
[40:08:14 -925749.786894] Model parameter optimization (eps = 1.000000)
[40:08:54 -925723.255568] SLOW spr round 1 (radius: 5)
[40:14:05 -925585.992291] SLOW spr round 2 (radius: 5)
[40:19:18 -925576.221232] SLOW spr round 3 (radius: 5)
[40:24:34 -925573.930034] SLOW spr round 4 (radius: 5)
[40:29:41 -925573.926928] SLOW spr round 5 (radius: 10)
[40:35:20 -925570.559781] SLOW spr round 6 (radius: 5)
[40:41:47 -925570.558933] SLOW spr round 7 (radius: 10)
[40:48:23 -925570.558436] SLOW spr round 8 (radius: 15)
[40:58:24 -925570.558015] SLOW spr round 9 (radius: 20)
[41:15:00 -925570.557643] SLOW spr round 10 (radius: 25)
[41:36:31 -925570.508495] Model parameter optimization (eps = 0.100000)

[41:36:57] ML tree search #12, logLikelihood: -925569.482557

[41:36:57 -4288170.164535] Initial branch length optimization
[41:37:23 -3435827.730331] Model parameter optimization (eps = 10.000000)
[41:39:39 -3429684.495060] AUTODETECT spr round 1 (radius: 5)
[41:44:55 -2148725.599602] AUTODETECT spr round 2 (radius: 10)
[41:50:29 -1526807.145648] AUTODETECT spr round 3 (radius: 15)
[41:56:20 -1234309.899956] AUTODETECT spr round 4 (radius: 20)
[42:03:07 -1097601.121031] AUTODETECT spr round 5 (radius: 25)
[42:11:17 -1036860.549047] SPR radius for FAST iterations: 25 (autodetect)
[42:11:17 -1036860.549047] Model parameter optimization (eps = 3.000000)
[42:12:50 -1034152.670745] FAST spr round 1 (radius: 25)
[42:22:10 -929176.142121] FAST spr round 2 (radius: 25)
[42:28:56 -925970.285082] FAST spr round 3 (radius: 25)
[42:34:08 -925802.931023] FAST spr round 4 (radius: 25)
[42:38:22 -925799.954638] FAST spr round 5 (radius: 25)
[42:42:08 -925797.747986] FAST spr round 6 (radius: 25)
[42:45:39 -925797.736138] Model parameter optimization (eps = 1.000000)
[42:46:21 -925758.698257] SLOW spr round 1 (radius: 5)
[42:51:32 -925561.521193] SLOW spr round 2 (radius: 5)
[42:56:44 -925559.881818] SLOW spr round 3 (radius: 5)
[43:01:42 -925559.809147] SLOW spr round 4 (radius: 10)
[43:07:18 -925556.711887] SLOW spr round 5 (radius: 5)
[43:13:40 -925556.710400] SLOW spr round 6 (radius: 10)
[43:20:18 -925555.856290] SLOW spr round 7 (radius: 5)
[43:26:42 -925555.227158] SLOW spr round 8 (radius: 5)
[43:32:17 -925555.224205] SLOW spr round 9 (radius: 10)
[43:38:12 -925555.222655] SLOW spr round 10 (radius: 15)
[43:48:34 -925555.221772] SLOW spr round 11 (radius: 20)
[44:05:11 -925555.221199] SLOW spr round 12 (radius: 25)
[44:26:53 -925555.220764] Model parameter optimization (eps = 0.100000)

[44:27:20] ML tree search #13, logLikelihood: -925554.768020

[44:27:20 -4217399.598961] Initial branch length optimization
[44:27:46 -3430087.914147] Model parameter optimization (eps = 10.000000)
[44:30:24 -3423264.982481] AUTODETECT spr round 1 (radius: 5)
[44:36:16 -2153122.482410] AUTODETECT spr round 2 (radius: 10)
[44:41:46 -1494864.838357] AUTODETECT spr round 3 (radius: 15)
[44:47:53 -1208249.093737] AUTODETECT spr round 4 (radius: 20)
[44:54:59 -1062099.886397] AUTODETECT spr round 5 (radius: 25)
[45:04:48 -1040939.345912] SPR radius for FAST iterations: 25 (autodetect)
[45:04:48 -1040939.345912] Model parameter optimization (eps = 3.000000)
[45:06:14 -1038173.530211] FAST spr round 1 (radius: 25)
[45:17:04 -931116.238411] FAST spr round 2 (radius: 25)
[45:25:32 -925989.231318] FAST spr round 3 (radius: 25)
[45:31:56 -925773.000137] FAST spr round 4 (radius: 25)
[45:37:00 -925759.132432] FAST spr round 5 (radius: 25)
[45:41:23 -925759.092856] Model parameter optimization (eps = 1.000000)
[45:42:09 -925717.789127] SLOW spr round 1 (radius: 5)
[45:48:33 -925589.423242] SLOW spr round 2 (radius: 5)
[45:54:33 -925561.764692] SLOW spr round 3 (radius: 5)
[45:59:44 -925559.219034] SLOW spr round 4 (radius: 5)
[46:04:47 -925559.206750] SLOW spr round 5 (radius: 10)
[46:10:29 -925558.345421] SLOW spr round 6 (radius: 5)
[46:17:01 -925557.713660] SLOW spr round 7 (radius: 5)
[46:22:40 -925557.710631] SLOW spr round 8 (radius: 10)
[46:28:39 -925557.708999] SLOW spr round 9 (radius: 15)
[46:39:16 -925557.708074] SLOW spr round 10 (radius: 20)
[46:56:19 -925557.707574] SLOW spr round 11 (radius: 25)
[47:18:00 -925557.707258] Model parameter optimization (eps = 0.100000)

[47:18:24] ML tree search #14, logLikelihood: -925557.318013

[47:18:25 -4222083.137606] Initial branch length optimization
[47:18:50 -3416583.659790] Model parameter optimization (eps = 10.000000)
[47:21:17 -3410165.568250] AUTODETECT spr round 1 (radius: 5)
[47:26:20 -2099985.631439] AUTODETECT spr round 2 (radius: 10)
[47:31:47 -1479703.826670] AUTODETECT spr round 3 (radius: 15)
[47:37:41 -1246774.293542] AUTODETECT spr round 4 (radius: 20)
[47:44:06 -1071366.910882] AUTODETECT spr round 5 (radius: 25)
[47:51:45 -1037240.588927] SPR radius for FAST iterations: 25 (autodetect)
[47:51:45 -1037240.588927] Model parameter optimization (eps = 3.000000)
[47:53:09 -1034646.070481] FAST spr round 1 (radius: 25)
[48:02:29 -929413.482042] FAST spr round 2 (radius: 25)
[48:09:19 -925955.006130] FAST spr round 3 (radius: 25)
[48:14:31 -925805.352218] FAST spr round 4 (radius: 25)
[48:18:57 -925784.283617] FAST spr round 5 (radius: 25)
[48:22:48 -925758.559123] FAST spr round 6 (radius: 25)
[48:26:22 -925758.557299] Model parameter optimization (eps = 1.000000)
[48:27:03 -925725.408439] SLOW spr round 1 (radius: 5)
[48:32:40 -925597.318597] SLOW spr round 2 (radius: 5)
[48:37:55 -925576.109631] SLOW spr round 3 (radius: 5)
[48:43:05 -925569.514445] SLOW spr round 4 (radius: 5)
[48:48:06 -925569.488068] SLOW spr round 5 (radius: 10)
[48:53:54 -925566.186438] SLOW spr round 6 (radius: 5)
[49:00:26 -925566.184681] SLOW spr round 7 (radius: 10)
[49:07:15 -925566.183433] SLOW spr round 8 (radius: 15)
[49:17:50 -925565.466626] SLOW spr round 9 (radius: 5)
[49:24:43 -925565.249139] SLOW spr round 10 (radius: 5)
[49:30:34 -925565.247935] SLOW spr round 11 (radius: 10)
[49:36:47 -925565.246876] SLOW spr round 12 (radius: 15)
[49:47:26 -925565.245967] SLOW spr round 13 (radius: 20)
[50:05:25 -925565.245215] SLOW spr round 14 (radius: 25)
[50:28:08 -925565.244594] Model parameter optimization (eps = 0.100000)

[50:28:43] ML tree search #15, logLikelihood: -925563.118631

[50:28:43 -4239149.403034] Initial branch length optimization
[50:29:06 -3442320.864399] Model parameter optimization (eps = 10.000000)
[50:31:17 -3435248.248670] AUTODETECT spr round 1 (radius: 5)
[50:36:14 -2173028.447347] AUTODETECT spr round 2 (radius: 10)
[50:41:32 -1477555.738232] AUTODETECT spr round 3 (radius: 15)
[50:47:16 -1141386.882804] AUTODETECT spr round 4 (radius: 20)
[50:53:39 -1072348.521484] AUTODETECT spr round 5 (radius: 25)
[51:01:55 -1032159.977484] SPR radius for FAST iterations: 25 (autodetect)
[51:01:55 -1032159.977484] Model parameter optimization (eps = 3.000000)
[51:03:44 -1029860.552634] FAST spr round 1 (radius: 25)
[51:12:30 -934460.591316] FAST spr round 2 (radius: 25)
[51:19:04 -926217.453676] FAST spr round 3 (radius: 25)
[51:24:03 -925843.421420] FAST spr round 4 (radius: 25)
[51:28:19 -925815.683887] FAST spr round 5 (radius: 25)
[51:32:00 -925815.633464] Model parameter optimization (eps = 1.000000)
[51:32:37 -925782.355746] SLOW spr round 1 (radius: 5)
[51:37:53 -925600.335672] SLOW spr round 2 (radius: 5)
[51:43:07 -925595.645920] SLOW spr round 3 (radius: 5)
[51:48:21 -925590.608233] SLOW spr round 4 (radius: 5)
[51:53:25 -925590.577529] SLOW spr round 5 (radius: 10)
[51:59:16 -925563.351545] SLOW spr round 6 (radius: 5)
[52:05:58 -925560.152675] SLOW spr round 7 (radius: 5)
[52:11:50 -925559.514347] SLOW spr round 8 (radius: 5)
[52:17:14 -925559.513411] SLOW spr round 9 (radius: 10)
[52:23:08 -925558.627240] SLOW spr round 10 (radius: 5)
[52:29:37 -925557.996513] SLOW spr round 11 (radius: 5)
[52:35:20 -925557.993565] SLOW spr round 12 (radius: 10)
[52:41:29 -925557.991954] SLOW spr round 13 (radius: 15)
[52:52:18 -925557.361249] SLOW spr round 14 (radius: 5)
[52:59:15 -925557.133216] SLOW spr round 15 (radius: 5)
[53:05:12 -925557.132251] SLOW spr round 16 (radius: 10)
[53:11:30 -925557.131361] SLOW spr round 17 (radius: 15)
[53:22:04 -925557.130554] SLOW spr round 18 (radius: 20)
[53:40:01 -925557.129838] SLOW spr round 19 (radius: 25)
[54:02:54 -925557.129198] Model parameter optimization (eps = 0.100000)

[54:03:19] ML tree search #16, logLikelihood: -925555.973145

[54:03:19 -4252005.161037] Initial branch length optimization
[54:03:43 -3418497.707352] Model parameter optimization (eps = 10.000000)
[54:05:59 -3412847.390933] AUTODETECT spr round 1 (radius: 5)
[54:10:56 -2147714.104612] AUTODETECT spr round 2 (radius: 10)
[54:16:16 -1516433.246408] AUTODETECT spr round 3 (radius: 15)
[54:22:18 -1187929.825613] AUTODETECT spr round 4 (radius: 20)
[54:28:53 -1074295.027172] AUTODETECT spr round 5 (radius: 25)
[54:36:53 -1040136.079529] SPR radius for FAST iterations: 25 (autodetect)
[54:36:53 -1040136.079529] Model parameter optimization (eps = 3.000000)
[54:38:25 -1037311.833384] FAST spr round 1 (radius: 25)
[54:47:34 -929991.627275] FAST spr round 2 (radius: 25)
[54:54:29 -925943.841980] FAST spr round 3 (radius: 25)
[54:59:48 -925790.371721] FAST spr round 4 (radius: 25)
[55:03:58 -925760.397824] FAST spr round 5 (radius: 25)
[55:07:36 -925760.206038] FAST spr round 6 (radius: 25)
[55:11:04 -925760.143076] Model parameter optimization (eps = 1.000000)
[55:11:55 -925681.629851] SLOW spr round 1 (radius: 5)
[55:17:07 -925566.061154] SLOW spr round 2 (radius: 5)
[55:22:24 -925557.301341] SLOW spr round 3 (radius: 5)
[55:27:36 -925557.209397] SLOW spr round 4 (radius: 10)
[55:33:27 -925552.867091] SLOW spr round 5 (radius: 5)
[55:40:04 -925552.648555] SLOW spr round 6 (radius: 5)
[55:45:49 -925552.635651] SLOW spr round 7 (radius: 10)
[55:51:53 -925552.342016] SLOW spr round 8 (radius: 5)
[55:58:16 -925552.339885] SLOW spr round 9 (radius: 10)
[56:04:48 -925552.338728] SLOW spr round 10 (radius: 15)
[56:15:09 -925550.856179] SLOW spr round 11 (radius: 5)
[56:22:03 -925550.855250] SLOW spr round 12 (radius: 10)
[56:29:11 -925550.854396] SLOW spr round 13 (radius: 15)
[56:39:31 -925550.853610] SLOW spr round 14 (radius: 20)
[56:57:10 -925550.852887] SLOW spr round 15 (radius: 25)
[57:19:25 -925550.801537] Model parameter optimization (eps = 0.100000)

[57:19:53] ML tree search #17, logLikelihood: -925550.334360

[57:19:53 -4210410.542538] Initial branch length optimization
[57:20:18 -3416597.665090] Model parameter optimization (eps = 10.000000)
[57:22:23 -3409134.200021] AUTODETECT spr round 1 (radius: 5)
[57:27:30 -2141613.617410] AUTODETECT spr round 2 (radius: 10)
[57:33:01 -1496437.325923] AUTODETECT spr round 3 (radius: 15)
[57:38:47 -1219267.549457] AUTODETECT spr round 4 (radius: 20)
[57:45:42 -1085291.603893] AUTODETECT spr round 5 (radius: 25)
[57:54:44 -1047465.788505] SPR radius for FAST iterations: 25 (autodetect)
[57:54:44 -1047465.788505] Model parameter optimization (eps = 3.000000)
[57:56:11 -1045132.115885] FAST spr round 1 (radius: 25)
[58:05:36 -929758.502862] FAST spr round 2 (radius: 25)
[58:12:15 -926161.259223] FAST spr round 3 (radius: 25)
[58:17:12 -925788.502353] FAST spr round 4 (radius: 25)
[58:21:22 -925771.068544] FAST spr round 5 (radius: 25)
[58:25:04 -925771.041290] Model parameter optimization (eps = 1.000000)
[58:25:43 -925710.995246] SLOW spr round 1 (radius: 5)
[58:30:54 -925549.194651] SLOW spr round 2 (radius: 5)
[58:36:12 -925544.685987] SLOW spr round 3 (radius: 5)
[58:41:14 -925544.672134] SLOW spr round 4 (radius: 10)
[58:46:59 -925541.201478] SLOW spr round 5 (radius: 5)
[58:53:29 -925540.657004] SLOW spr round 6 (radius: 5)
[58:59:15 -925540.643968] SLOW spr round 7 (radius: 10)
[59:05:19 -925540.643368] SLOW spr round 8 (radius: 15)
[59:15:47 -925540.642904] SLOW spr round 9 (radius: 20)
[59:32:33 -925540.599216] SLOW spr round 10 (radius: 25)
[59:54:16 -925540.548255] Model parameter optimization (eps = 0.100000)

[59:54:49] ML tree search #18, logLikelihood: -925538.702287

[59:54:49 -4211252.409024] Initial branch length optimization
[59:55:15 -3419285.603095] Model parameter optimization (eps = 10.000000)
[59:57:48 -3412003.339913] AUTODETECT spr round 1 (radius: 5)
[60:03:01 -2155228.881211] AUTODETECT spr round 2 (radius: 10)
[60:08:42 -1425099.184155] AUTODETECT spr round 3 (radius: 15)
[60:14:26 -1156436.865147] AUTODETECT spr round 4 (radius: 20)
[60:20:48 -1048259.700225] AUTODETECT spr round 5 (radius: 25)
[60:28:14 -1023836.491152] SPR radius for FAST iterations: 25 (autodetect)
[60:28:14 -1023836.491152] Model parameter optimization (eps = 3.000000)
[60:29:41 -1021244.473476] FAST spr round 1 (radius: 25)
[60:38:51 -929116.506872] FAST spr round 2 (radius: 25)
[60:45:38 -926002.160607] FAST spr round 3 (radius: 25)
[60:51:07 -925706.670713] FAST spr round 4 (radius: 25)
[60:55:35 -925672.013608] FAST spr round 5 (radius: 25)
[60:59:20 -925645.233792] FAST spr round 6 (radius: 25)
[61:02:53 -925645.195984] Model parameter optimization (eps = 1.000000)
[61:03:30 -925619.531720] SLOW spr round 1 (radius: 5)
[61:08:46 -925542.956987] SLOW spr round 2 (radius: 5)
[61:13:57 -925537.070877] SLOW spr round 3 (radius: 5)
[61:19:00 -925536.909689] SLOW spr round 4 (radius: 5)
[61:23:58 -925536.908943] SLOW spr round 5 (radius: 10)
[61:29:44 -925532.064597] SLOW spr round 6 (radius: 5)
[61:36:07 -925531.788379] SLOW spr round 7 (radius: 5)
[61:41:50 -925531.776228] SLOW spr round 8 (radius: 10)
[61:47:51 -925531.775107] SLOW spr round 9 (radius: 15)
[61:58:18 -925531.774080] SLOW spr round 10 (radius: 20)
[62:15:00 -925531.773142] SLOW spr round 11 (radius: 25)
[62:36:33 -925531.724656] Model parameter optimization (eps = 0.100000)

[62:36:54] ML tree search #19, logLikelihood: -925531.401723

[62:36:55 -4245023.596264] Initial branch length optimization
[62:37:19 -3436987.717717] Model parameter optimization (eps = 10.000000)
[62:39:39 -3429820.430701] AUTODETECT spr round 1 (radius: 5)
[62:44:42 -2048462.342861] AUTODETECT spr round 2 (radius: 10)
[62:50:06 -1403320.765940] AUTODETECT spr round 3 (radius: 15)
[62:55:59 -1178586.944438] AUTODETECT spr round 4 (radius: 20)
[63:02:35 -1079079.308769] AUTODETECT spr round 5 (radius: 25)
[63:10:43 -1032200.465376] SPR radius for FAST iterations: 25 (autodetect)
[63:10:43 -1032200.465376] Model parameter optimization (eps = 3.000000)
[63:12:10 -1029999.303827] FAST spr round 1 (radius: 25)
[63:20:32 -928129.289123] FAST spr round 2 (radius: 25)
[63:26:53 -925948.668619] FAST spr round 3 (radius: 25)
[63:32:16 -925811.298492] FAST spr round 4 (radius: 25)
[63:36:28 -925804.980577] FAST spr round 5 (radius: 25)
[63:40:12 -925804.944858] Model parameter optimization (eps = 1.000000)
[63:40:52 -925737.171070] SLOW spr round 1 (radius: 5)
[63:46:09 -925615.241816] SLOW spr round 2 (radius: 5)
[63:51:20 -925605.592557] SLOW spr round 3 (radius: 5)
[63:56:29 -925604.799447] SLOW spr round 4 (radius: 5)
[64:01:28 -925604.797883] SLOW spr round 5 (radius: 10)
[64:07:14 -925602.023783] SLOW spr round 6 (radius: 5)
[64:13:43 -925601.791963] SLOW spr round 7 (radius: 5)
[64:19:23 -925601.711450] SLOW spr round 8 (radius: 10)
[64:25:25 -925601.660379] SLOW spr round 9 (radius: 15)
[64:36:13 -925601.650354] SLOW spr round 10 (radius: 20)
[64:54:46 -925601.597892] SLOW spr round 11 (radius: 25)
[65:18:23 -925601.595929] Model parameter optimization (eps = 0.100000)

[65:18:58] ML tree search #20, logLikelihood: -925600.195089


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.231679,0.494931) (0.127727,0.638344) (0.419244,0.729064) (0.221350,2.250485) 
   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: -925531.401723

AIC score: 1855072.803446 / AICc score: 1857444.283398 / BIC score: 1868293.339952
Free parameters (model + branch lengths): 2005

Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P21817/3_mltree/P21817.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P21817/3_mltree/P21817.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P21817/3_mltree/P21817.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P21817/3_mltree/P21817.raxml.log

Analysis started: 13-Jul-2021 22:14:45 / finished: 16-Jul-2021 15:33:44

Elapsed time: 235138.867 seconds

Consumed energy: 21416.139 Wh (= 107 km in an electric car, or 535 km with an e-scooter!)