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

System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 11-Jul-2021 16:26:01 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5FYA8/2_msa/Q5FYA8_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5FYA8/3_mltree/Q5FYA8 --seed 2 --threads 7 --tree rand{20} pars{20}

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

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5FYA8/2_msa/Q5FYA8_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 452 sites

WARNING: Sequences tr_F1PHF0_F1PHF0_CANLF_9615 and sp_Q32KH5_GALNS_CANLF_9615 are exactly identical!
WARNING: Sequences tr_K7CLG1_K7CLG1_PANTR_9598 and tr_A0A2R8ZGT3_A0A2R8ZGT3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A1D5R654_A0A1D5R654_MACMU_9544 and tr_A0A2I3LME9_A0A2I3LME9_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5R654_A0A1D5R654_MACMU_9544 and tr_A0A2K5NQH1_A0A2K5NQH1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5R654_A0A1D5R654_MACMU_9544 and tr_A0A2K6DNA4_A0A2K6DNA4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5R654_A0A1D5R654_MACMU_9544 and tr_A0A2K5YDV4_A0A2K5YDV4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H9H4P4_H9H4P4_MACMU_9544 and tr_G7Q247_G7Q247_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A8XD87_A8XD87_CAEBR_6238 and tr_A0A2G5T5T5_A0A2G5T5T5_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_R7TCT9_R7TCT9_CAPTE_283909 and tr_R7VB05_R7VB05_CAPTE_283909 are exactly identical!
WARNING: Sequences tr_A0A096N0B6_A0A096N0B6_PAPAN_9555 and tr_A0A2K5YHM5_A0A2K5YHM5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A094EHI0_A0A094EHI0_9PEZI_1420912 and tr_A0A1B8GPK7_A0A1B8GPK7_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A2D0S7M7_A0A2D0S7M7_ICTPU_7998 and tr_A0A2D0S7N6_A0A2D0S7N6_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0S7M7_A0A2D0S7M7_ICTPU_7998 and tr_A0A2D0S7N7_A0A2D0S7N7_ICTPU_7998 are exactly identical!
WARNING: Duplicate sequences found: 13

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5FYA8/3_mltree/Q5FYA8.raxml.reduced.phy

Alignment comprises 1 partitions and 452 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 452 / 452
Gaps: 16.29 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5FYA8/3_mltree/Q5FYA8.raxml.rba

Parallelization scheme autoconfig: 1 worker(s) x 7 thread(s)

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

[00:00:00] Generating 20 random starting tree(s) with 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 65 / 5200
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -744802.688598] Initial branch length optimization
[00:00:03 -626464.147944] Model parameter optimization (eps = 10.000000)
[00:00:22 -623517.093058] AUTODETECT spr round 1 (radius: 5)
[00:02:04 -467601.523865] AUTODETECT spr round 2 (radius: 10)
[00:03:59 -356664.715605] AUTODETECT spr round 3 (radius: 15)
[00:06:04 -298972.107987] AUTODETECT spr round 4 (radius: 20)
[00:08:23 -280132.322768] AUTODETECT spr round 5 (radius: 25)
[00:11:04 -278360.490179] SPR radius for FAST iterations: 25 (autodetect)
[00:11:04 -278360.490179] Model parameter optimization (eps = 3.000000)
[00:11:09 -278358.636452] FAST spr round 1 (radius: 25)
[00:13:39 -252842.685734] FAST spr round 2 (radius: 25)
[00:15:38 -251484.703107] FAST spr round 3 (radius: 25)
[00:17:25 -251360.847333] FAST spr round 4 (radius: 25)
[00:18:58 -251343.142554] FAST spr round 5 (radius: 25)
[00:20:36 -250837.212428] FAST spr round 6 (radius: 25)
[00:22:13 -248238.547113] FAST spr round 7 (radius: 25)
[00:23:49 -248056.923857] FAST spr round 8 (radius: 25)
[00:25:19 -247897.522001] FAST spr round 9 (radius: 25)
[00:26:46 -247897.520958] Model parameter optimization (eps = 1.000000)
[00:26:50 -247896.788422] SLOW spr round 1 (radius: 5)
[00:28:50 -247799.095938] SLOW spr round 2 (radius: 5)
[00:30:48 -247786.867618] SLOW spr round 3 (radius: 5)
[00:32:42 -247783.813532] SLOW spr round 4 (radius: 5)
[00:34:35 -247783.264797] SLOW spr round 5 (radius: 5)
[00:36:27 -247783.264758] SLOW spr round 6 (radius: 10)
[00:38:20 -247782.830158] SLOW spr round 7 (radius: 5)
[00:40:39 -247782.830130] SLOW spr round 8 (radius: 10)
[00:42:44 -247782.830128] SLOW spr round 9 (radius: 15)
[00:45:31 -247750.433549] SLOW spr round 10 (radius: 5)
[00:47:57 -247697.788845] SLOW spr round 11 (radius: 5)
[00:50:07 -247692.390084] SLOW spr round 12 (radius: 5)
[00:52:05 -247692.390051] SLOW spr round 13 (radius: 10)
[00:54:01 -247692.390044] SLOW spr round 14 (radius: 15)
[00:56:57 -247692.390042] SLOW spr round 15 (radius: 20)
[01:01:05 -247692.218951] SLOW spr round 16 (radius: 5)
[01:03:29 -247692.193983] SLOW spr round 17 (radius: 10)
[01:05:41 -247692.193542] SLOW spr round 18 (radius: 15)
[01:08:25 -247692.193448] SLOW spr round 19 (radius: 20)
[01:12:36 -247692.193428] SLOW spr round 20 (radius: 25)
[01:17:49 -247692.193424] Model parameter optimization (eps = 0.100000)

[01:17:54] ML tree search #1, logLikelihood: -247692.155896

[01:17:54 -744156.265385] Initial branch length optimization
[01:17:57 -623818.877419] Model parameter optimization (eps = 10.000000)
[01:18:21 -620992.113264] AUTODETECT spr round 1 (radius: 5)
[01:20:06 -464340.883466] AUTODETECT spr round 2 (radius: 10)
[01:22:02 -371149.044415] AUTODETECT spr round 3 (radius: 15)
[01:24:11 -322619.055220] AUTODETECT spr round 4 (radius: 20)
[01:26:45 -290756.698546] AUTODETECT spr round 5 (radius: 25)
[01:29:39 -279807.323371] SPR radius for FAST iterations: 25 (autodetect)
[01:29:39 -279807.323371] Model parameter optimization (eps = 3.000000)
[01:29:55 -279694.182452] FAST spr round 1 (radius: 25)
[01:32:31 -248707.599634] FAST spr round 2 (radius: 25)
[01:34:35 -247867.273638] FAST spr round 3 (radius: 25)
[01:36:24 -247785.668918] FAST spr round 4 (radius: 25)
[01:38:01 -247777.388190] FAST spr round 5 (radius: 25)
[01:39:32 -247776.027529] FAST spr round 6 (radius: 25)
[01:41:02 -247776.027505] Model parameter optimization (eps = 1.000000)
[01:41:10 -247775.239795] SLOW spr round 1 (radius: 5)
[01:43:16 -247694.143803] SLOW spr round 2 (radius: 5)
[01:45:15 -247684.978848] SLOW spr round 3 (radius: 5)
[01:47:11 -247683.373249] SLOW spr round 4 (radius: 5)
[01:49:04 -247681.820855] SLOW spr round 5 (radius: 5)
[01:50:57 -247681.378798] SLOW spr round 6 (radius: 5)
[01:52:49 -247680.757178] SLOW spr round 7 (radius: 5)
[01:54:42 -247680.757176] SLOW spr round 8 (radius: 10)
[01:56:38 -247676.726414] SLOW spr round 9 (radius: 5)
[01:59:01 -247663.523237] SLOW spr round 10 (radius: 5)
[02:01:10 -247655.225280] SLOW spr round 11 (radius: 5)
[02:03:09 -247653.601939] SLOW spr round 12 (radius: 5)
[02:05:04 -247653.177809] SLOW spr round 13 (radius: 5)
[02:06:56 -247653.177677] SLOW spr round 14 (radius: 10)
[02:08:52 -247653.161342] SLOW spr round 15 (radius: 15)
[02:11:57 -247653.160603] SLOW spr round 16 (radius: 20)
[02:16:21 -247653.160583] SLOW spr round 17 (radius: 25)
[02:22:13 -247653.160581] Model parameter optimization (eps = 0.100000)

[02:22:25] ML tree search #2, logLikelihood: -247652.805187

[02:22:25 -748134.570380] Initial branch length optimization
[02:22:28 -624626.516520] Model parameter optimization (eps = 10.000000)
[02:22:51 -621804.277653] AUTODETECT spr round 1 (radius: 5)
[02:24:38 -467395.934237] AUTODETECT spr round 2 (radius: 10)
[02:26:38 -350992.958794] AUTODETECT spr round 3 (radius: 15)
[02:28:38 -305565.954803] AUTODETECT spr round 4 (radius: 20)
[02:30:58 -283990.558796] AUTODETECT spr round 5 (radius: 25)
[02:33:41 -278402.438786] SPR radius for FAST iterations: 25 (autodetect)
[02:33:41 -278402.438786] Model parameter optimization (eps = 3.000000)
[02:33:46 -278401.595557] FAST spr round 1 (radius: 25)
[02:36:19 -248800.746803] FAST spr round 2 (radius: 25)
[02:38:25 -247925.463259] FAST spr round 3 (radius: 25)
[02:40:18 -247830.334863] FAST spr round 4 (radius: 25)
[02:41:56 -247818.923242] FAST spr round 5 (radius: 25)
[02:43:28 -247818.917549] Model parameter optimization (eps = 1.000000)
[02:43:31 -247818.893526] SLOW spr round 1 (radius: 5)
[02:45:41 -247737.240058] SLOW spr round 2 (radius: 5)
[02:47:46 -247725.215664] SLOW spr round 3 (radius: 5)
[02:49:44 -247723.455618] SLOW spr round 4 (radius: 5)
[02:51:40 -247723.453792] SLOW spr round 5 (radius: 10)
[02:53:38 -247720.081421] SLOW spr round 6 (radius: 5)
[02:56:00 -247719.066402] SLOW spr round 7 (radius: 5)
[02:58:07 -247719.066395] SLOW spr round 8 (radius: 10)
[03:00:08 -247719.066394] SLOW spr round 9 (radius: 15)
[03:03:09 -247718.914000] SLOW spr round 10 (radius: 5)
[03:05:36 -247718.053946] SLOW spr round 11 (radius: 5)
[03:07:46 -247716.628947] SLOW spr round 12 (radius: 5)
[03:09:47 -247716.628918] SLOW spr round 13 (radius: 10)
[03:11:46 -247716.628917] SLOW spr round 14 (radius: 15)
[03:14:50 -247716.628917] SLOW spr round 15 (radius: 20)
[03:19:13 -247716.628917] SLOW spr round 16 (radius: 25)
[03:24:45 -247716.628917] Model parameter optimization (eps = 0.100000)

[03:24:48] ML tree search #3, logLikelihood: -247716.626515

[03:24:49 -741215.670579] Initial branch length optimization
[03:24:52 -624402.259172] Model parameter optimization (eps = 10.000000)
[03:25:21 -621496.390792] AUTODETECT spr round 1 (radius: 5)
[03:27:07 -465595.420006] AUTODETECT spr round 2 (radius: 10)
[03:29:05 -353778.030371] AUTODETECT spr round 3 (radius: 15)
[03:31:13 -298227.390498] AUTODETECT spr round 4 (radius: 20)
[03:33:41 -283686.403999] AUTODETECT spr round 5 (radius: 25)
[03:36:18 -277190.089941] SPR radius for FAST iterations: 25 (autodetect)
[03:36:18 -277190.089941] Model parameter optimization (eps = 3.000000)
[03:36:23 -277188.667618] FAST spr round 1 (radius: 25)
[03:39:03 -249112.001707] FAST spr round 2 (radius: 25)
[03:41:08 -247882.470696] FAST spr round 3 (radius: 25)
[03:43:00 -247790.809356] FAST spr round 4 (radius: 25)
[03:44:36 -247785.035624] FAST spr round 5 (radius: 25)
[03:46:08 -247784.994624] Model parameter optimization (eps = 1.000000)
[03:46:13 -247784.747633] SLOW spr round 1 (radius: 5)
[03:48:23 -247707.948882] SLOW spr round 2 (radius: 5)
[03:50:24 -247701.743310] SLOW spr round 3 (radius: 5)
[03:52:19 -247701.743027] SLOW spr round 4 (radius: 10)
[03:54:16 -247698.358730] SLOW spr round 5 (radius: 5)
[03:56:39 -247697.367282] SLOW spr round 6 (radius: 5)
[03:58:44 -247697.367146] SLOW spr round 7 (radius: 10)
[04:00:44 -247697.367142] SLOW spr round 8 (radius: 15)
[04:03:41 -247695.352478] SLOW spr round 9 (radius: 5)
[04:06:08 -247691.419581] SLOW spr round 10 (radius: 5)
[04:08:17 -247691.418917] SLOW spr round 11 (radius: 10)
[04:10:17 -247691.418744] SLOW spr round 12 (radius: 15)
[04:13:07 -247691.418691] SLOW spr round 13 (radius: 20)
[04:17:00 -247691.418675] SLOW spr round 14 (radius: 25)
[04:21:47 -247691.418670] Model parameter optimization (eps = 0.100000)

[04:21:50] ML tree search #4, logLikelihood: -247691.398594

[04:21:51 -741255.551002] Initial branch length optimization
[04:21:53 -622990.772505] Model parameter optimization (eps = 10.000000)
[04:22:18 -620163.345021] AUTODETECT spr round 1 (radius: 5)
[04:24:05 -464028.057850] AUTODETECT spr round 2 (radius: 10)
[04:26:05 -350757.609789] AUTODETECT spr round 3 (radius: 15)
[04:28:13 -316576.875851] AUTODETECT spr round 4 (radius: 20)
[04:30:41 -287396.138161] AUTODETECT spr round 5 (radius: 25)
[04:33:34 -281059.179675] SPR radius for FAST iterations: 25 (autodetect)
[04:33:34 -281059.179675] Model parameter optimization (eps = 3.000000)
[04:33:49 -280958.501225] FAST spr round 1 (radius: 25)
[04:36:24 -249225.992514] FAST spr round 2 (radius: 25)
[04:38:29 -247879.322303] FAST spr round 3 (radius: 25)
[04:40:20 -247766.096843] FAST spr round 4 (radius: 25)
[04:42:00 -247735.103542] FAST spr round 5 (radius: 25)
[04:43:36 -247731.764964] FAST spr round 6 (radius: 25)
[04:45:08 -247731.759701] Model parameter optimization (eps = 1.000000)
[04:45:22 -247729.607937] SLOW spr round 1 (radius: 5)
[04:47:29 -247665.345023] SLOW spr round 2 (radius: 5)
[04:49:33 -247652.083669] SLOW spr round 3 (radius: 5)
[04:51:31 -247648.771835] SLOW spr round 4 (radius: 5)
[04:53:28 -247648.771814] SLOW spr round 5 (radius: 10)
[04:55:26 -247648.771800] SLOW spr round 6 (radius: 15)
[04:58:39 -247648.771788] SLOW spr round 7 (radius: 20)
[05:03:09 -247648.771775] SLOW spr round 8 (radius: 25)
[05:09:11 -247648.771763] Model parameter optimization (eps = 0.100000)

[05:09:19] ML tree search #5, logLikelihood: -247648.634126

[05:09:19 -738413.049394] Initial branch length optimization
[05:09:22 -622804.778665] Model parameter optimization (eps = 10.000000)
[05:09:43 -620035.612376] AUTODETECT spr round 1 (radius: 5)
[05:11:30 -463953.087637] AUTODETECT spr round 2 (radius: 10)
[05:13:27 -359029.004251] AUTODETECT spr round 3 (radius: 15)
[05:15:35 -300497.268308] AUTODETECT spr round 4 (radius: 20)
[05:18:03 -278374.849376] AUTODETECT spr round 5 (radius: 25)
[05:20:55 -276096.778521] SPR radius for FAST iterations: 25 (autodetect)
[05:20:55 -276096.778521] Model parameter optimization (eps = 3.000000)
[05:21:16 -276012.802978] FAST spr round 1 (radius: 25)
[05:23:50 -248860.325905] FAST spr round 2 (radius: 25)
[05:25:53 -247898.657218] FAST spr round 3 (radius: 25)
[05:27:45 -247754.098951] FAST spr round 4 (radius: 25)
[05:29:24 -247733.578921] FAST spr round 5 (radius: 25)
[05:30:57 -247730.727709] FAST spr round 6 (radius: 25)
[05:32:28 -247730.726504] Model parameter optimization (eps = 1.000000)
[05:32:39 -247729.978172] SLOW spr round 1 (radius: 5)
[05:34:46 -247675.418545] SLOW spr round 2 (radius: 5)
[05:36:49 -247659.595482] SLOW spr round 3 (radius: 5)
[05:38:47 -247659.595234] SLOW spr round 4 (radius: 10)
[05:40:47 -247658.176071] SLOW spr round 5 (radius: 5)
[05:43:12 -247658.175973] SLOW spr round 6 (radius: 10)
[05:45:23 -247657.038212] SLOW spr round 7 (radius: 5)
[05:47:46 -247648.550359] SLOW spr round 8 (radius: 5)
[05:49:55 -247647.445803] SLOW spr round 9 (radius: 5)
[05:51:56 -247647.445795] SLOW spr round 10 (radius: 10)
[05:53:54 -247647.445795] SLOW spr round 11 (radius: 15)
[05:57:06 -247638.626446] SLOW spr round 12 (radius: 5)
[05:59:33 -247638.626295] SLOW spr round 13 (radius: 10)
[06:01:48 -247638.626288] SLOW spr round 14 (radius: 15)
[06:04:48 -247638.626286] SLOW spr round 15 (radius: 20)
[06:09:27 -247638.626286] SLOW spr round 16 (radius: 25)
[06:15:26 -247638.626286] Model parameter optimization (eps = 0.100000)

[06:15:31] ML tree search #6, logLikelihood: -247638.573354

[06:15:31 -742965.146773] Initial branch length optimization
[06:15:33 -622966.452712] Model parameter optimization (eps = 10.000000)
[06:15:57 -619965.477338] AUTODETECT spr round 1 (radius: 5)
[06:17:42 -460485.530261] AUTODETECT spr round 2 (radius: 10)
[06:19:39 -354250.150199] AUTODETECT spr round 3 (radius: 15)
[06:21:45 -310741.752859] AUTODETECT spr round 4 (radius: 20)
[06:24:17 -287398.596961] AUTODETECT spr round 5 (radius: 25)
[06:27:06 -281380.507795] SPR radius for FAST iterations: 25 (autodetect)
[06:27:06 -281380.507795] Model parameter optimization (eps = 3.000000)
[06:27:11 -281379.709773] FAST spr round 1 (radius: 25)
[06:29:54 -249488.945993] FAST spr round 2 (radius: 25)
[06:32:03 -247977.980069] FAST spr round 3 (radius: 25)
[06:33:56 -247862.699685] FAST spr round 4 (radius: 25)
[06:35:34 -247844.186327] FAST spr round 5 (radius: 25)
[06:37:06 -247844.185902] Model parameter optimization (eps = 1.000000)
[06:37:21 -247770.966178] SLOW spr round 1 (radius: 5)
[06:39:33 -247717.726037] SLOW spr round 2 (radius: 5)
[06:41:40 -247691.275637] SLOW spr round 3 (radius: 5)
[06:43:44 -247681.443070] SLOW spr round 4 (radius: 5)
[06:45:44 -247668.899881] SLOW spr round 5 (radius: 5)
[06:47:38 -247668.898275] SLOW spr round 6 (radius: 10)
[06:49:38 -247662.513070] SLOW spr round 7 (radius: 5)
[06:51:59 -247653.548371] SLOW spr round 8 (radius: 5)
[06:54:06 -247653.548212] SLOW spr round 9 (radius: 10)
[06:56:07 -247653.548167] SLOW spr round 10 (radius: 15)
[06:59:13 -247653.548140] SLOW spr round 11 (radius: 20)
[07:03:50 -247653.103856] SLOW spr round 12 (radius: 5)
[07:06:17 -247653.103216] SLOW spr round 13 (radius: 10)
[07:08:34 -247653.103188] SLOW spr round 14 (radius: 15)
[07:11:30 -247653.103179] SLOW spr round 15 (radius: 20)
[07:16:11 -247653.103171] SLOW spr round 16 (radius: 25)
[07:22:15 -247653.103164] Model parameter optimization (eps = 0.100000)

[07:22:23] ML tree search #7, logLikelihood: -247652.865601

[07:22:23 -740261.612183] Initial branch length optimization
[07:22:27 -622996.094019] Model parameter optimization (eps = 10.000000)
[07:22:50 -620109.892616] AUTODETECT spr round 1 (radius: 5)
[07:24:35 -466986.204125] AUTODETECT spr round 2 (radius: 10)
[07:26:30 -376119.846282] AUTODETECT spr round 3 (radius: 15)
[07:28:42 -313620.681425] AUTODETECT spr round 4 (radius: 20)
[07:31:13 -280664.621405] AUTODETECT spr round 5 (radius: 25)
[07:33:55 -278194.893862] SPR radius for FAST iterations: 25 (autodetect)
[07:33:55 -278194.893862] Model parameter optimization (eps = 3.000000)
[07:34:00 -278193.858704] FAST spr round 1 (radius: 25)
[07:36:32 -249054.613206] FAST spr round 2 (radius: 25)
[07:38:35 -247973.556545] FAST spr round 3 (radius: 25)
[07:40:24 -247871.217833] FAST spr round 4 (radius: 25)
[07:42:01 -247855.446571] FAST spr round 5 (radius: 25)
[07:43:33 -247851.646332] FAST spr round 6 (radius: 25)
[07:45:04 -247850.933767] FAST spr round 7 (radius: 25)
[07:46:34 -247850.933730] Model parameter optimization (eps = 1.000000)
[07:46:49 -247806.931809] SLOW spr round 1 (radius: 5)
[07:48:56 -247704.036420] SLOW spr round 2 (radius: 5)
[07:50:59 -247667.260553] SLOW spr round 3 (radius: 5)
[07:52:58 -247663.447315] SLOW spr round 4 (radius: 5)
[07:54:53 -247663.445115] SLOW spr round 5 (radius: 10)
[07:56:51 -247655.976143] SLOW spr round 6 (radius: 5)
[07:59:16 -247651.377060] SLOW spr round 7 (radius: 5)
[08:01:24 -247651.026581] SLOW spr round 8 (radius: 5)
[08:03:25 -247651.026578] SLOW spr round 9 (radius: 10)
[08:05:22 -247651.026578] SLOW spr round 10 (radius: 15)
[08:08:21 -247651.026578] SLOW spr round 11 (radius: 20)
[08:12:26 -247651.026578] SLOW spr round 12 (radius: 25)
[08:17:17 -247651.026578] Model parameter optimization (eps = 0.100000)

[08:17:25] ML tree search #8, logLikelihood: -247650.864995

[08:17:25 -739336.625208] Initial branch length optimization
[08:17:28 -620708.142207] Model parameter optimization (eps = 10.000000)
[08:17:53 -617823.019878] AUTODETECT spr round 1 (radius: 5)
[08:19:38 -466657.834480] AUTODETECT spr round 2 (radius: 10)
[08:21:34 -349997.608526] AUTODETECT spr round 3 (radius: 15)
[08:23:45 -300689.829641] AUTODETECT spr round 4 (radius: 20)
[08:26:09 -279889.231465] AUTODETECT spr round 5 (radius: 25)
[08:29:00 -276337.519872] SPR radius for FAST iterations: 25 (autodetect)
[08:29:00 -276337.519872] Model parameter optimization (eps = 3.000000)
[08:29:06 -276336.185596] FAST spr round 1 (radius: 25)
[08:31:47 -248866.247856] FAST spr round 2 (radius: 25)
[08:33:50 -247895.226146] FAST spr round 3 (radius: 25)
[08:35:40 -247825.426021] FAST spr round 4 (radius: 25)
[08:37:14 -247822.451058] FAST spr round 5 (radius: 25)
[08:38:45 -247822.450743] Model parameter optimization (eps = 1.000000)
[08:38:49 -247822.334681] SLOW spr round 1 (radius: 5)
[08:40:55 -247755.835001] SLOW spr round 2 (radius: 5)
[08:42:57 -247743.765857] SLOW spr round 3 (radius: 5)
[08:44:55 -247740.772583] SLOW spr round 4 (radius: 5)
[08:46:50 -247740.772305] SLOW spr round 5 (radius: 10)
[08:48:48 -247737.778722] SLOW spr round 6 (radius: 5)
[08:51:10 -247734.817747] SLOW spr round 7 (radius: 5)
[08:53:18 -247729.748050] SLOW spr round 8 (radius: 5)
[08:55:18 -247729.748048] SLOW spr round 9 (radius: 10)
[08:57:16 -247729.748048] SLOW spr round 10 (radius: 15)
[09:00:22 -247729.748047] SLOW spr round 11 (radius: 20)
[09:04:54 -247729.407565] SLOW spr round 12 (radius: 5)
[09:07:20 -247729.406324] SLOW spr round 13 (radius: 10)
[09:09:35 -247729.406271] SLOW spr round 14 (radius: 15)
[09:12:29 -247729.406264] SLOW spr round 15 (radius: 20)
[09:17:08 -247729.406263] SLOW spr round 16 (radius: 25)
[09:23:04 -247729.406263] Model parameter optimization (eps = 0.100000)

[09:23:10] ML tree search #9, logLikelihood: -247729.379482

[09:23:10 -744994.757036] Initial branch length optimization
[09:23:13 -624978.809362] Model parameter optimization (eps = 10.000000)
[09:23:41 -622076.734067] AUTODETECT spr round 1 (radius: 5)
[09:25:28 -464009.187341] AUTODETECT spr round 2 (radius: 10)
[09:27:27 -354310.944991] AUTODETECT spr round 3 (radius: 15)
[09:29:30 -321108.218697] AUTODETECT spr round 4 (radius: 20)
[09:32:10 -282068.870496] AUTODETECT spr round 5 (radius: 25)
[09:35:25 -277795.169889] SPR radius for FAST iterations: 25 (autodetect)
[09:35:25 -277795.169889] Model parameter optimization (eps = 3.000000)
[09:35:30 -277794.317325] FAST spr round 1 (radius: 25)
[09:38:10 -249343.246508] FAST spr round 2 (radius: 25)
[09:40:13 -247855.754718] FAST spr round 3 (radius: 25)
[09:42:01 -247803.790442] FAST spr round 4 (radius: 25)
[09:43:37 -247798.075878] FAST spr round 5 (radius: 25)
[09:45:09 -247798.075357] Model parameter optimization (eps = 1.000000)
[09:45:13 -247797.971317] SLOW spr round 1 (radius: 5)
[09:47:24 -247742.075781] SLOW spr round 2 (radius: 5)
[09:49:26 -247734.890545] SLOW spr round 3 (radius: 5)
[09:51:23 -247723.243349] SLOW spr round 4 (radius: 5)
[09:53:20 -247718.033217] SLOW spr round 5 (radius: 5)
[09:55:14 -247718.032817] SLOW spr round 6 (radius: 10)
[09:57:11 -247716.181345] SLOW spr round 7 (radius: 5)
[09:59:32 -247715.906887] SLOW spr round 8 (radius: 5)
[10:01:40 -247715.906811] SLOW spr round 9 (radius: 10)
[10:03:41 -247715.867192] SLOW spr round 10 (radius: 15)
[10:06:43 -247715.863677] SLOW spr round 11 (radius: 20)
[10:11:07 -247714.341277] SLOW spr round 12 (radius: 5)
[10:13:39 -247712.204594] SLOW spr round 13 (radius: 5)
[10:15:50 -247712.201630] SLOW spr round 14 (radius: 10)
[10:17:52 -247712.201014] SLOW spr round 15 (radius: 15)
[10:20:50 -247712.200883] SLOW spr round 16 (radius: 20)
[10:25:13 -247712.200855] SLOW spr round 17 (radius: 25)
[10:30:44 -247712.200849] Model parameter optimization (eps = 0.100000)

[10:30:48] ML tree search #10, logLikelihood: -247712.191079

[10:30:48 -742003.501201] Initial branch length optimization
[10:30:50 -624714.196868] Model parameter optimization (eps = 10.000000)
[10:31:17 -621675.273585] AUTODETECT spr round 1 (radius: 5)
[10:33:02 -476083.176550] AUTODETECT spr round 2 (radius: 10)
[10:34:58 -376327.271801] AUTODETECT spr round 3 (radius: 15)
[10:37:11 -318847.892266] AUTODETECT spr round 4 (radius: 20)
[10:39:34 -287515.383658] AUTODETECT spr round 5 (radius: 25)
[10:42:13 -282475.475752] SPR radius for FAST iterations: 25 (autodetect)
[10:42:13 -282475.475752] Model parameter optimization (eps = 3.000000)
[10:42:19 -282474.392963] FAST spr round 1 (radius: 25)
[10:44:59 -248920.374930] FAST spr round 2 (radius: 25)
[10:47:00 -247974.089244] FAST spr round 3 (radius: 25)
[10:48:47 -247908.375262] FAST spr round 4 (radius: 25)
[10:50:26 -247888.326404] FAST spr round 5 (radius: 25)
[10:52:01 -247877.943321] FAST spr round 6 (radius: 25)
[10:53:32 -247876.421093] FAST spr round 7 (radius: 25)
[10:55:03 -247870.564360] FAST spr round 8 (radius: 25)
[10:56:31 -247870.564360] Model parameter optimization (eps = 1.000000)
[10:56:35 -247870.469686] SLOW spr round 1 (radius: 5)
[10:58:38 -247814.209852] SLOW spr round 2 (radius: 5)
[11:00:40 -247796.653600] SLOW spr round 3 (radius: 5)
[11:02:36 -247791.296649] SLOW spr round 4 (radius: 5)
[11:04:34 -247786.059118] SLOW spr round 5 (radius: 5)
[11:06:27 -247785.304622] SLOW spr round 6 (radius: 5)
[11:08:20 -247785.304619] SLOW spr round 7 (radius: 10)
[11:10:18 -247783.909209] SLOW spr round 8 (radius: 5)
[11:12:39 -247783.898089] SLOW spr round 9 (radius: 10)
[11:14:48 -247783.895673] SLOW spr round 10 (radius: 15)
[11:17:49 -247783.895152] SLOW spr round 11 (radius: 20)
[11:22:37 -247783.895041] SLOW spr round 12 (radius: 25)
[11:28:39 -247783.895018] Model parameter optimization (eps = 0.100000)

[11:28:51] ML tree search #11, logLikelihood: -247695.593282

[11:28:51 -741299.703502] Initial branch length optimization
[11:28:54 -623749.976083] Model parameter optimization (eps = 10.000000)
[11:29:22 -620941.273786] AUTODETECT spr round 1 (radius: 5)
[11:31:08 -468838.045863] AUTODETECT spr round 2 (radius: 10)
[11:33:06 -359962.107089] AUTODETECT spr round 3 (radius: 15)
[11:35:12 -315765.343162] AUTODETECT spr round 4 (radius: 20)
[11:37:42 -290919.527642] AUTODETECT spr round 5 (radius: 25)
[11:40:48 -284257.437123] SPR radius for FAST iterations: 25 (autodetect)
[11:40:48 -284257.437123] Model parameter optimization (eps = 3.000000)
[11:41:06 -284168.519246] FAST spr round 1 (radius: 25)
[11:43:42 -249039.087648] FAST spr round 2 (radius: 25)
[11:45:45 -247934.784276] FAST spr round 3 (radius: 25)
[11:47:32 -247787.793325] FAST spr round 4 (radius: 25)
[11:49:09 -247765.801766] FAST spr round 5 (radius: 25)
[11:50:40 -247765.202381] FAST spr round 6 (radius: 25)
[11:52:09 -247765.202124] Model parameter optimization (eps = 1.000000)
[11:52:21 -247762.948138] SLOW spr round 1 (radius: 5)
[11:54:26 -247684.684959] SLOW spr round 2 (radius: 5)
[11:56:30 -247668.964643] SLOW spr round 3 (radius: 5)
[11:58:27 -247665.567134] SLOW spr round 4 (radius: 5)
[12:00:21 -247665.566909] SLOW spr round 5 (radius: 10)
[12:02:19 -247661.231728] SLOW spr round 6 (radius: 5)
[12:04:41 -247652.210898] SLOW spr round 7 (radius: 5)
[12:06:47 -247652.210814] SLOW spr round 8 (radius: 10)
[12:08:48 -247652.210789] SLOW spr round 9 (radius: 15)
[12:11:49 -247652.210764] SLOW spr round 10 (radius: 20)
[12:16:10 -247651.796865] SLOW spr round 11 (radius: 5)
[12:18:38 -247651.796216] SLOW spr round 12 (radius: 10)
[12:20:54 -247651.796173] SLOW spr round 13 (radius: 15)
[12:23:46 -247651.796149] SLOW spr round 14 (radius: 20)
[12:28:10 -247651.796126] SLOW spr round 15 (radius: 25)
[12:33:29 -247651.796103] Model parameter optimization (eps = 0.100000)

[12:33:37] ML tree search #12, logLikelihood: -247651.412528

[12:33:37 -742079.675912] Initial branch length optimization
[12:33:40 -623663.078176] Model parameter optimization (eps = 10.000000)
[12:34:01 -620805.805525] AUTODETECT spr round 1 (radius: 5)
[12:35:48 -465619.593244] AUTODETECT spr round 2 (radius: 10)
[12:37:45 -358460.538570] AUTODETECT spr round 3 (radius: 15)
[12:39:52 -309977.973223] AUTODETECT spr round 4 (radius: 20)
[12:42:09 -281392.796505] AUTODETECT spr round 5 (radius: 25)
[12:44:50 -276166.310658] SPR radius for FAST iterations: 25 (autodetect)
[12:44:50 -276166.310658] Model parameter optimization (eps = 3.000000)
[12:45:16 -276031.078444] FAST spr round 1 (radius: 25)
[12:47:52 -248778.362789] FAST spr round 2 (radius: 25)
[12:49:57 -247857.062194] FAST spr round 3 (radius: 25)
[12:51:48 -247776.009319] FAST spr round 4 (radius: 25)
[12:53:23 -247763.045136] FAST spr round 5 (radius: 25)
[12:54:55 -247763.044908] Model parameter optimization (eps = 1.000000)
[12:55:09 -247761.752124] SLOW spr round 1 (radius: 5)
[12:57:18 -247686.192593] SLOW spr round 2 (radius: 5)
[12:59:21 -247663.301066] SLOW spr round 3 (radius: 5)
[13:01:16 -247663.211954] SLOW spr round 4 (radius: 10)
[13:03:12 -247660.970965] SLOW spr round 5 (radius: 5)
[13:05:35 -247656.591790] SLOW spr round 6 (radius: 5)
[13:07:43 -247655.598336] SLOW spr round 7 (radius: 5)
[13:09:42 -247654.437570] SLOW spr round 8 (radius: 5)
[13:11:37 -247654.437483] SLOW spr round 9 (radius: 10)
[13:13:33 -247654.437379] SLOW spr round 10 (radius: 15)
[13:16:34 -247653.736090] SLOW spr round 11 (radius: 5)
[13:18:55 -247653.727738] SLOW spr round 12 (radius: 10)
[13:21:04 -247653.727012] SLOW spr round 13 (radius: 15)
[13:23:52 -247653.726950] SLOW spr round 14 (radius: 20)
[13:28:11 -247653.726945] SLOW spr round 15 (radius: 25)
[13:33:34 -247653.726944] Model parameter optimization (eps = 0.100000)

[13:33:37] ML tree search #13, logLikelihood: -247653.704244

[13:33:37 -741285.546937] Initial branch length optimization
[13:33:40 -620413.017602] Model parameter optimization (eps = 10.000000)
[13:34:05 -617678.251675] AUTODETECT spr round 1 (radius: 5)
[13:35:50 -464506.449970] AUTODETECT spr round 2 (radius: 10)
[13:37:51 -352957.161314] AUTODETECT spr round 3 (radius: 15)
[13:39:57 -308729.016822] AUTODETECT spr round 4 (radius: 20)
[13:42:36 -284806.418436] AUTODETECT spr round 5 (radius: 25)
[13:45:39 -281696.752542] SPR radius for FAST iterations: 25 (autodetect)
[13:45:39 -281696.752542] Model parameter optimization (eps = 3.000000)
[13:45:57 -281583.992285] FAST spr round 1 (radius: 25)
[13:48:34 -249165.651164] FAST spr round 2 (radius: 25)
[13:50:35 -247875.828392] FAST spr round 3 (radius: 25)
[13:52:21 -247768.314161] FAST spr round 4 (radius: 25)
[13:53:58 -247753.611671] FAST spr round 5 (radius: 25)
[13:55:31 -247746.287498] FAST spr round 6 (radius: 25)
[13:57:02 -247737.401206] FAST spr round 7 (radius: 25)
[13:58:32 -247733.017551] FAST spr round 8 (radius: 25)
[14:00:01 -247733.016830] Model parameter optimization (eps = 1.000000)
[14:00:05 -247732.201035] SLOW spr round 1 (radius: 5)
[14:02:10 -247664.656731] SLOW spr round 2 (radius: 5)
[14:04:12 -247652.108993] SLOW spr round 3 (radius: 5)
[14:06:08 -247649.278065] SLOW spr round 4 (radius: 5)
[14:08:03 -247649.276820] SLOW spr round 5 (radius: 10)
[14:09:59 -247645.468252] SLOW spr round 6 (radius: 5)
[14:12:22 -247643.583257] SLOW spr round 7 (radius: 5)
[14:14:30 -247643.583168] SLOW spr round 8 (radius: 10)
[14:16:30 -247643.583117] SLOW spr round 9 (radius: 15)
[14:19:36 -247643.543211] SLOW spr round 10 (radius: 20)
[14:24:09 -247643.541625] SLOW spr round 11 (radius: 25)
[14:30:05 -247643.541521] Model parameter optimization (eps = 0.100000)

[14:30:18] ML tree search #14, logLikelihood: -247629.118507

[14:30:18 -745878.964729] Initial branch length optimization
[14:30:20 -624866.998536] Model parameter optimization (eps = 10.000000)
[14:30:43 -622031.970472] AUTODETECT spr round 1 (radius: 5)
[14:32:31 -464895.202656] AUTODETECT spr round 2 (radius: 10)
[14:34:29 -364270.664901] AUTODETECT spr round 3 (radius: 15)
[14:36:38 -312846.993364] AUTODETECT spr round 4 (radius: 20)
[14:39:11 -289984.412921] AUTODETECT spr round 5 (radius: 25)
[14:41:49 -281551.494473] SPR radius for FAST iterations: 25 (autodetect)
[14:41:49 -281551.494473] Model parameter optimization (eps = 3.000000)
[14:41:53 -281550.583757] FAST spr round 1 (radius: 25)
[14:44:32 -249481.355335] FAST spr round 2 (radius: 25)
[14:46:37 -247984.919039] FAST spr round 3 (radius: 25)
[14:48:28 -247839.878659] FAST spr round 4 (radius: 25)
[14:50:06 -247816.449567] FAST spr round 5 (radius: 25)
[14:51:40 -247812.454430] FAST spr round 6 (radius: 25)
[14:53:09 -247812.454359] Model parameter optimization (eps = 1.000000)
[14:53:13 -247812.214557] SLOW spr round 1 (radius: 5)
[14:55:23 -247740.817520] SLOW spr round 2 (radius: 5)
[14:57:25 -247723.847985] SLOW spr round 3 (radius: 5)
[14:59:21 -247723.471600] SLOW spr round 4 (radius: 5)
[15:01:15 -247723.471265] SLOW spr round 5 (radius: 10)
[15:03:12 -247721.397620] SLOW spr round 6 (radius: 5)
[15:05:33 -247718.563510] SLOW spr round 7 (radius: 5)
[15:07:40 -247716.768204] SLOW spr round 8 (radius: 5)
[15:09:39 -247716.768111] SLOW spr round 9 (radius: 10)
[15:11:38 -247716.768110] SLOW spr round 10 (radius: 15)
[15:14:51 -247716.768110] SLOW spr round 11 (radius: 20)
[15:19:49 -247716.728337] SLOW spr round 12 (radius: 25)
[15:26:16 -247716.727020] Model parameter optimization (eps = 0.100000)

[15:26:20] ML tree search #15, logLikelihood: -247716.688640

[15:26:20 -740895.731631] Initial branch length optimization
[15:26:23 -621891.178357] Model parameter optimization (eps = 10.000000)
[15:26:43 -618999.068697] AUTODETECT spr round 1 (radius: 5)
[15:28:29 -471424.636150] AUTODETECT spr round 2 (radius: 10)
[15:30:26 -355568.165958] AUTODETECT spr round 3 (radius: 15)
[15:32:33 -302313.237331] AUTODETECT spr round 4 (radius: 20)
[15:35:03 -285456.188727] AUTODETECT spr round 5 (radius: 25)
[15:37:38 -279986.134881] SPR radius for FAST iterations: 25 (autodetect)
[15:37:38 -279986.134881] Model parameter optimization (eps = 3.000000)
[15:37:43 -279984.655359] FAST spr round 1 (radius: 25)
[15:40:21 -249334.939516] FAST spr round 2 (radius: 25)
[15:42:28 -247947.865092] FAST spr round 3 (radius: 25)
[15:44:19 -247858.846300] FAST spr round 4 (radius: 25)
[15:46:01 -247834.030114] FAST spr round 5 (radius: 25)
[15:47:34 -247830.340657] FAST spr round 6 (radius: 25)
[15:49:03 -247830.340481] Model parameter optimization (eps = 1.000000)
[15:49:07 -247830.315333] SLOW spr round 1 (radius: 5)
[15:51:13 -247749.973698] SLOW spr round 2 (radius: 5)
[15:53:14 -247727.228288] SLOW spr round 3 (radius: 5)
[15:55:09 -247726.587567] SLOW spr round 4 (radius: 5)
[15:57:04 -247726.585455] SLOW spr round 5 (radius: 10)
[15:59:00 -247726.466170] SLOW spr round 6 (radius: 5)
[16:01:22 -247726.465946] SLOW spr round 7 (radius: 10)
[16:03:31 -247725.847559] SLOW spr round 8 (radius: 5)
[16:05:51 -247725.847293] SLOW spr round 9 (radius: 10)
[16:07:59 -247725.847260] SLOW spr round 10 (radius: 15)
[16:11:01 -247721.947822] SLOW spr round 11 (radius: 5)
[16:13:31 -247712.990426] SLOW spr round 12 (radius: 5)
[16:15:41 -247712.990398] SLOW spr round 13 (radius: 10)
[16:17:43 -247712.990395] SLOW spr round 14 (radius: 15)
[16:20:45 -247712.990395] SLOW spr round 15 (radius: 20)
[16:25:08 -247712.990394] SLOW spr round 16 (radius: 25)
[16:30:48 -247712.990394] Model parameter optimization (eps = 0.100000)

[16:31:08] ML tree search #16, logLikelihood: -247648.880642

[16:31:08 -746806.449127] Initial branch length optimization
[16:31:11 -626334.246846] Model parameter optimization (eps = 10.000000)
[16:31:34 -623422.382895] AUTODETECT spr round 1 (radius: 5)
[16:33:19 -471793.564089] AUTODETECT spr round 2 (radius: 10)
[16:35:13 -363756.554685] AUTODETECT spr round 3 (radius: 15)
[16:37:20 -316581.509992] AUTODETECT spr round 4 (radius: 20)
[16:39:53 -288066.863158] AUTODETECT spr round 5 (radius: 25)
[16:43:01 -282406.562209] SPR radius for FAST iterations: 25 (autodetect)
[16:43:01 -282406.562209] Model parameter optimization (eps = 3.000000)
[16:43:22 -282215.836911] FAST spr round 1 (radius: 25)
[16:46:01 -249199.911276] FAST spr round 2 (radius: 25)
[16:48:06 -247862.555217] FAST spr round 3 (radius: 25)
[16:49:58 -247782.008163] FAST spr round 4 (radius: 25)
[16:51:39 -247769.291107] FAST spr round 5 (radius: 25)
[16:53:16 -247763.775240] FAST spr round 6 (radius: 25)
[16:54:47 -247763.064952] FAST spr round 7 (radius: 25)
[16:56:17 -247760.838761] FAST spr round 8 (radius: 25)
[16:57:46 -247760.838696] Model parameter optimization (eps = 1.000000)
[16:57:58 -247758.918468] SLOW spr round 1 (radius: 5)
[17:00:09 -247678.062491] SLOW spr round 2 (radius: 5)
[17:02:11 -247671.882496] SLOW spr round 3 (radius: 5)
[17:04:07 -247671.169747] SLOW spr round 4 (radius: 5)
[17:06:02 -247671.169610] SLOW spr round 5 (radius: 10)
[17:07:59 -247670.018918] SLOW spr round 6 (radius: 5)
[17:10:22 -247665.446217] SLOW spr round 7 (radius: 5)
[17:12:29 -247665.445131] SLOW spr round 8 (radius: 10)
[17:14:28 -247665.445073] SLOW spr round 9 (radius: 15)
[17:17:29 -247665.445067] SLOW spr round 10 (radius: 20)
[17:21:54 -247665.042221] SLOW spr round 11 (radius: 5)
[17:24:22 -247665.041619] SLOW spr round 12 (radius: 10)
[17:26:37 -247665.041599] SLOW spr round 13 (radius: 15)
[17:29:28 -247665.041599] SLOW spr round 14 (radius: 20)
[17:33:57 -247665.041599] SLOW spr round 15 (radius: 25)
[17:39:41 -247665.041598] Model parameter optimization (eps = 0.100000)

[17:39:50] ML tree search #17, logLikelihood: -247664.783816

[17:39:50 -745466.852479] Initial branch length optimization
[17:39:54 -625207.015733] Model parameter optimization (eps = 10.000000)
[17:40:19 -622320.023969] AUTODETECT spr round 1 (radius: 5)
[17:42:06 -467319.114085] AUTODETECT spr round 2 (radius: 10)
[17:44:02 -364218.428843] AUTODETECT spr round 3 (radius: 15)
[17:46:13 -306517.684814] AUTODETECT spr round 4 (radius: 20)
[17:48:57 -286260.404269] AUTODETECT spr round 5 (radius: 25)
[17:52:21 -284094.172055] SPR radius for FAST iterations: 25 (autodetect)
[17:52:22 -284094.172055] Model parameter optimization (eps = 3.000000)
[17:52:26 -284093.099363] FAST spr round 1 (radius: 25)
[17:55:12 -250006.038435] FAST spr round 2 (radius: 25)
[17:57:19 -247921.905310] FAST spr round 3 (radius: 25)
[17:59:10 -247821.885716] FAST spr round 4 (radius: 25)
[18:00:46 -247813.326352] FAST spr round 5 (radius: 25)
[18:02:17 -247813.326310] Model parameter optimization (eps = 1.000000)
[18:02:21 -247813.258494] SLOW spr round 1 (radius: 5)
[18:04:29 -247757.361330] SLOW spr round 2 (radius: 5)
[18:06:32 -247738.831109] SLOW spr round 3 (radius: 5)
[18:08:25 -247738.830645] SLOW spr round 4 (radius: 10)
[18:10:21 -247737.543223] SLOW spr round 5 (radius: 5)
[18:12:39 -247737.052501] SLOW spr round 6 (radius: 5)
[18:14:43 -247737.052418] SLOW spr round 7 (radius: 10)
[18:16:41 -247737.052405] SLOW spr round 8 (radius: 15)
[18:19:41 -247737.052401] SLOW spr round 9 (radius: 20)
[18:24:05 -247737.052399] SLOW spr round 10 (radius: 25)
[18:29:48 -247737.052398] Model parameter optimization (eps = 0.100000)

[18:29:51] ML tree search #18, logLikelihood: -247737.049191

[18:29:51 -739695.557736] Initial branch length optimization
[18:29:54 -622379.867540] Model parameter optimization (eps = 10.000000)
[18:30:17 -619552.055577] AUTODETECT spr round 1 (radius: 5)
[18:32:04 -468355.197795] AUTODETECT spr round 2 (radius: 10)
[18:34:00 -371386.934804] AUTODETECT spr round 3 (radius: 15)
[18:36:06 -316410.711547] AUTODETECT spr round 4 (radius: 20)
[18:38:36 -280755.310434] AUTODETECT spr round 5 (radius: 25)
[18:41:23 -278569.766329] SPR radius for FAST iterations: 25 (autodetect)
[18:41:23 -278569.766329] Model parameter optimization (eps = 3.000000)
[18:41:27 -278569.269994] FAST spr round 1 (radius: 25)
[18:44:01 -248985.783117] FAST spr round 2 (radius: 25)
[18:46:09 -247956.509734] FAST spr round 3 (radius: 25)
[18:48:01 -247857.788837] FAST spr round 4 (radius: 25)
[18:49:42 -247839.794271] FAST spr round 5 (radius: 25)
[18:51:15 -247836.483374] FAST spr round 6 (radius: 25)
[18:52:46 -247836.311830] FAST spr round 7 (radius: 25)
[18:54:16 -247836.311633] Model parameter optimization (eps = 1.000000)
[18:54:20 -247836.144244] SLOW spr round 1 (radius: 5)
[18:56:28 -247752.672836] SLOW spr round 2 (radius: 5)
[18:58:32 -247741.120363] SLOW spr round 3 (radius: 5)
[19:00:34 -247733.817789] SLOW spr round 4 (radius: 5)
[19:02:30 -247733.816596] SLOW spr round 5 (radius: 10)
[19:04:27 -247733.580564] SLOW spr round 6 (radius: 5)
[19:06:51 -247727.232998] SLOW spr round 7 (radius: 5)
[19:09:02 -247726.105160] SLOW spr round 8 (radius: 5)
[19:11:04 -247726.105148] SLOW spr round 9 (radius: 10)
[19:13:03 -247726.105148] SLOW spr round 10 (radius: 15)
[19:16:09 -247726.105148] SLOW spr round 11 (radius: 20)
[19:20:38 -247726.105148] SLOW spr round 12 (radius: 25)
[19:26:18 -247726.105148] Model parameter optimization (eps = 0.100000)

[19:26:23] ML tree search #19, logLikelihood: -247726.010779

[19:26:23 -744204.333093] Initial branch length optimization
[19:26:25 -623488.106738] Model parameter optimization (eps = 10.000000)
[19:26:58 -620487.945910] AUTODETECT spr round 1 (radius: 5)
[19:28:44 -461155.238790] AUTODETECT spr round 2 (radius: 10)
[19:30:39 -344565.195863] AUTODETECT spr round 3 (radius: 15)
[19:32:49 -287546.086274] AUTODETECT spr round 4 (radius: 20)
[19:35:05 -276931.777335] AUTODETECT spr round 5 (radius: 25)
[19:37:52 -275751.713563] SPR radius for FAST iterations: 25 (autodetect)
[19:37:52 -275751.713563] Model parameter optimization (eps = 3.000000)
[19:37:56 -275751.013077] FAST spr round 1 (radius: 25)
[19:40:25 -248747.403144] FAST spr round 2 (radius: 25)
[19:42:27 -247895.229581] FAST spr round 3 (radius: 25)
[19:44:13 -247828.620332] FAST spr round 4 (radius: 25)
[19:45:50 -247806.769498] FAST spr round 5 (radius: 25)
[19:47:22 -247800.677190] FAST spr round 6 (radius: 25)
[19:48:53 -247799.754355] FAST spr round 7 (radius: 25)
[19:50:23 -247794.569660] FAST spr round 8 (radius: 25)
[19:51:53 -247794.568060] Model parameter optimization (eps = 1.000000)
[19:51:57 -247793.973659] SLOW spr round 1 (radius: 5)
[19:53:58 -247730.388150] SLOW spr round 2 (radius: 5)
[19:55:56 -247728.726594] SLOW spr round 3 (radius: 5)
[19:57:51 -247726.682606] SLOW spr round 4 (radius: 5)
[19:59:45 -247724.151194] SLOW spr round 5 (radius: 5)
[20:01:38 -247724.151077] SLOW spr round 6 (radius: 10)
[20:03:34 -247724.151075] SLOW spr round 7 (radius: 15)
[20:06:37 -247724.003218] SLOW spr round 8 (radius: 5)
[20:09:00 -247723.977882] SLOW spr round 9 (radius: 10)
[20:11:10 -247723.977421] SLOW spr round 10 (radius: 15)
[20:13:59 -247723.977322] SLOW spr round 11 (radius: 20)
[20:18:19 -247723.977301] SLOW spr round 12 (radius: 25)
[20:23:44 -247723.977296] Model parameter optimization (eps = 0.100000)

[20:23:49] ML tree search #20, logLikelihood: -247723.974055


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.155164,0.434924) (0.249971,0.471072) (0.367491,0.906559) (0.227375,2.118130) 
   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: -247629.118507

AIC score: 499268.237015 / AICc score: 8543328.237015 / BIC score: 507516.169785
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=452).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 42 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5FYA8/3_mltree/Q5FYA8.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5FYA8/3_mltree/Q5FYA8.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5FYA8/3_mltree/Q5FYA8.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5FYA8/3_mltree/Q5FYA8.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q5FYA8/3_mltree/Q5FYA8.raxml.log

Analysis started: 11-Jul-2021 16:26:01 / finished: 12-Jul-2021 12:49:50

Elapsed time: 73429.471 seconds