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

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

RAxML-NG was called at 03-Jul-2021 18:05:49 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q2TAA5/2_msa/Q2TAA5_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q2TAA5/3_mltree/Q2TAA5 --seed 2 --threads 7 --tree rand{20} pars{20}

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

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q2TAA5/2_msa/Q2TAA5_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 489 sites

WARNING: Sequences tr_J3KCM2_J3KCM2_COCIM_246410 and tr_A0A0J6YHW8_A0A0J6YHW8_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6Q846_B6Q846_TALMQ_441960 and tr_A0A093VEV7_A0A093VEV7_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B2W1G6_B2W1G6_PYRTR_426418 and tr_A0A2W1EIT1_A0A2W1EIT1_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_C6H5I7_C6H5I7_AJECH_544712 and tr_F0U5V0_F0U5V0_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_Q2UN63_Q2UN63_ASPOR_510516 and tr_A0A1S9D6J7_A0A1S9D6J7_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A0E0JBM9_A0A0E0JBM9_ORYNI_4536 and tr_A0A0E0RJA4_A0A0E0RJA4_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0JBM9_A0A0E0JBM9_ORYNI_4536 and tr_A0A0E0BUK5_A0A0E0BUK5_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A2RB90_A2RB90_ASPNC_425011 and tr_A0A319A6Z4_A0A319A6Z4_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_G7XSY0_G7XSY0_ASPKW_1033177 and tr_A0A146F6H4_A0A146F6H4_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G7XSY0_G7XSY0_ASPKW_1033177 and tr_A0A317UP27_A0A317UP27_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_G2XXE0_G2XXE0_BOTF4_999810 and tr_M7U7T9_M7U7T9_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_A0A0D2Y928_A0A0D2Y928_FUSO4_426428 and tr_X0CPA7_X0CPA7_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_A0A0D2Y928_A0A0D2Y928_FUSO4_426428 and tr_A0A2H3GMC5_A0A2H3GMC5_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_V2XY25_V2XY25_MONRO_1381753 and tr_A0A0W0FCH8_A0A0W0FCH8_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_A0A094E551_A0A094E551_9PEZI_1420912 and tr_A0A1B8GLN0_A0A1B8GLN0_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_V4TBQ9_V4TBQ9_9ROSI_85681 and tr_A0A2H5NKL4_A0A2H5NKL4_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A0F0I7C0_A0A0F0I7C0_ASPPU_1403190 and tr_A0A2G7GBF9_A0A2G7GBF9_9EURO_656916 are exactly identical!
WARNING: Sequences tr_A0A117E2G0_A0A117E2G0_ASPNG_5061 and tr_A0A1L9NMG6_A0A1L9NMG6_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A1S4BMX5_A0A1S4BMX5_TOBAC_4097 and tr_A0A1U7XBA5_A0A1U7XBA5_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2K5P5B9_A0A2K5P5B9_CERAT_9531 and tr_A0A2K6A0C6_A0A2K6A0C6_MANLE_9568 are exactly identical!
WARNING: Duplicate sequences found: 20

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/Q2TAA5/3_mltree/Q2TAA5.raxml.reduced.phy

Alignment comprises 1 partitions and 489 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 489 / 489
Gaps: 11.54 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q2TAA5/3_mltree/Q2TAA5.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 / 70 / 5600
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -806659.008593] Initial branch length optimization
[00:00:04 -688582.433486] Model parameter optimization (eps = 10.000000)
[00:00:38 -686598.076691] AUTODETECT spr round 1 (radius: 5)
[00:02:33 -519715.897799] AUTODETECT spr round 2 (radius: 10)
[00:04:46 -412149.958632] AUTODETECT spr round 3 (radius: 15)
[00:07:07 -353643.767024] AUTODETECT spr round 4 (radius: 20)
[00:09:57 -335527.495770] AUTODETECT spr round 5 (radius: 25)
[00:13:38 -331484.402079] SPR radius for FAST iterations: 25 (autodetect)
[00:13:38 -331484.402079] Model parameter optimization (eps = 3.000000)
[00:13:42 -331483.823821] FAST spr round 1 (radius: 25)
[00:16:45 -303178.427959] FAST spr round 2 (radius: 25)
[00:19:01 -302096.355536] FAST spr round 3 (radius: 25)
[00:20:59 -302041.902455] FAST spr round 4 (radius: 25)
[00:22:47 -302025.048723] FAST spr round 5 (radius: 25)
[00:24:30 -302022.390049] FAST spr round 6 (radius: 25)
[00:26:08 -302022.389505] Model parameter optimization (eps = 1.000000)
[00:26:25 -301704.563020] SLOW spr round 1 (radius: 5)
[00:28:40 -301594.039166] SLOW spr round 2 (radius: 5)
[00:30:50 -301570.915389] SLOW spr round 3 (radius: 5)
[00:32:55 -301558.877650] SLOW spr round 4 (radius: 5)
[00:34:58 -301555.896308] SLOW spr round 5 (radius: 5)
[00:37:00 -301555.771789] SLOW spr round 6 (radius: 5)
[00:38:59 -301555.771147] SLOW spr round 7 (radius: 10)
[00:41:09 -301549.606848] SLOW spr round 8 (radius: 5)
[00:43:40 -301548.860814] SLOW spr round 9 (radius: 5)
[00:45:56 -301548.860573] SLOW spr round 10 (radius: 10)
[00:48:11 -301547.549609] SLOW spr round 11 (radius: 5)
[00:50:38 -301546.342951] SLOW spr round 12 (radius: 5)
[00:52:46 -301546.342659] SLOW spr round 13 (radius: 10)
[00:54:59 -301546.342448] SLOW spr round 14 (radius: 15)
[00:58:36 -301546.342248] SLOW spr round 15 (radius: 20)
[01:04:00 -301546.342048] SLOW spr round 16 (radius: 25)
[01:10:59 -301546.341849] Model parameter optimization (eps = 0.100000)

[01:11:03] ML tree search #1, logLikelihood: -301546.333461

[01:11:03 -807387.867720] Initial branch length optimization
[01:11:07 -689564.210611] Model parameter optimization (eps = 10.000000)
[01:11:49 -687397.594826] AUTODETECT spr round 1 (radius: 5)
[01:13:47 -520490.723533] AUTODETECT spr round 2 (radius: 10)
[01:16:04 -411745.004225] AUTODETECT spr round 3 (radius: 15)
[01:18:37 -355330.399897] AUTODETECT spr round 4 (radius: 20)
[01:21:27 -335281.772514] AUTODETECT spr round 5 (radius: 25)
[01:25:03 -332944.417757] SPR radius for FAST iterations: 25 (autodetect)
[01:25:03 -332944.417757] Model parameter optimization (eps = 3.000000)
[01:25:26 -332601.734129] FAST spr round 1 (radius: 25)
[01:28:44 -303052.889821] FAST spr round 2 (radius: 25)
[01:31:04 -301834.082187] FAST spr round 3 (radius: 25)
[01:33:11 -301720.447439] FAST spr round 4 (radius: 25)
[01:35:04 -301705.976953] FAST spr round 5 (radius: 25)
[01:36:52 -301696.190750] FAST spr round 6 (radius: 25)
[01:38:37 -301688.267992] FAST spr round 7 (radius: 25)
[01:40:21 -301688.266840] Model parameter optimization (eps = 1.000000)
[01:40:38 -301686.953589] SLOW spr round 1 (radius: 5)
[01:43:03 -301595.890570] SLOW spr round 2 (radius: 5)
[01:45:24 -301585.813778] SLOW spr round 3 (radius: 5)
[01:47:39 -301577.233769] SLOW spr round 4 (radius: 5)
[01:49:51 -301575.125788] SLOW spr round 5 (radius: 5)
[01:52:02 -301575.125433] SLOW spr round 6 (radius: 10)
[01:54:20 -301572.843466] SLOW spr round 7 (radius: 5)
[01:56:58 -301566.210776] SLOW spr round 8 (radius: 5)
[01:59:19 -301556.832205] SLOW spr round 9 (radius: 5)
[02:01:34 -301556.832130] SLOW spr round 10 (radius: 10)
[02:03:52 -301554.728555] SLOW spr round 11 (radius: 5)
[02:06:27 -301552.796895] SLOW spr round 12 (radius: 5)
[02:08:48 -301552.796831] SLOW spr round 13 (radius: 10)
[02:11:10 -301552.796828] SLOW spr round 14 (radius: 15)
[02:14:41 -301552.796827] SLOW spr round 15 (radius: 20)
[02:19:41 -301552.796826] SLOW spr round 16 (radius: 25)
[02:25:59 -301552.796825] Model parameter optimization (eps = 0.100000)

[02:26:13] ML tree search #2, logLikelihood: -301550.626612

[02:26:13 -806960.631295] Initial branch length optimization
[02:26:17 -690217.112078] Model parameter optimization (eps = 10.000000)
[02:26:57 -687926.189083] AUTODETECT spr round 1 (radius: 5)
[02:28:57 -529032.390618] AUTODETECT spr round 2 (radius: 10)
[02:31:13 -399223.597932] AUTODETECT spr round 3 (radius: 15)
[02:33:37 -356993.842454] AUTODETECT spr round 4 (radius: 20)
[02:36:17 -349185.976415] AUTODETECT spr round 5 (radius: 25)
[02:39:38 -338696.897679] SPR radius for FAST iterations: 25 (autodetect)
[02:39:38 -338696.897679] Model parameter optimization (eps = 3.000000)
[02:40:01 -338477.661580] FAST spr round 1 (radius: 25)
[02:43:19 -302821.782037] FAST spr round 2 (radius: 25)
[02:45:37 -301827.185762] FAST spr round 3 (radius: 25)
[02:47:39 -301707.999758] FAST spr round 4 (radius: 25)
[02:49:28 -301679.878377] FAST spr round 5 (radius: 25)
[02:51:11 -301670.910363] FAST spr round 6 (radius: 25)
[02:52:52 -301670.908795] Model parameter optimization (eps = 1.000000)
[02:53:07 -301662.232166] SLOW spr round 1 (radius: 5)
[02:55:31 -301545.290390] SLOW spr round 2 (radius: 5)
[02:57:50 -301520.535808] SLOW spr round 3 (radius: 5)
[02:59:58 -301520.535743] SLOW spr round 4 (radius: 10)
[03:02:14 -301513.727467] SLOW spr round 5 (radius: 5)
[03:04:50 -301506.726074] SLOW spr round 6 (radius: 5)
[03:07:10 -301506.725924] SLOW spr round 7 (radius: 10)
[03:09:30 -301506.725919] SLOW spr round 8 (radius: 15)
[03:13:02 -301505.063665] SLOW spr round 9 (radius: 5)
[03:15:41 -301505.063599] SLOW spr round 10 (radius: 10)
[03:18:15 -301505.063589] SLOW spr round 11 (radius: 15)
[03:21:37 -301505.063587] SLOW spr round 12 (radius: 20)
[03:26:43 -301505.063585] SLOW spr round 13 (radius: 25)
[03:33:01 -301505.063584] Model parameter optimization (eps = 0.100000)

[03:33:14] ML tree search #3, logLikelihood: -301503.965621

[03:33:15 -805138.978858] Initial branch length optimization
[03:33:18 -688662.075800] Model parameter optimization (eps = 10.000000)
[03:33:58 -686506.592751] AUTODETECT spr round 1 (radius: 5)
[03:35:58 -528769.744690] AUTODETECT spr round 2 (radius: 10)
[03:38:18 -400642.819772] AUTODETECT spr round 3 (radius: 15)
[03:40:39 -357690.970271] AUTODETECT spr round 4 (radius: 20)
[03:43:24 -339415.220016] AUTODETECT spr round 5 (radius: 25)
[03:46:26 -336895.158984] SPR radius for FAST iterations: 25 (autodetect)
[03:46:26 -336895.158984] Model parameter optimization (eps = 3.000000)
[03:46:50 -336612.229458] FAST spr round 1 (radius: 25)
[03:50:04 -302748.910290] FAST spr round 2 (radius: 25)
[03:52:26 -301782.108022] FAST spr round 3 (radius: 25)
[03:54:29 -301665.122476] FAST spr round 4 (radius: 25)
[03:56:19 -301662.382356] FAST spr round 5 (radius: 25)
[03:58:05 -301662.381343] Model parameter optimization (eps = 1.000000)
[03:58:14 -301661.446685] SLOW spr round 1 (radius: 5)
[04:00:37 -301547.264200] SLOW spr round 2 (radius: 5)
[04:02:57 -301524.230229] SLOW spr round 3 (radius: 5)
[04:05:11 -301521.685628] SLOW spr round 4 (radius: 5)
[04:07:22 -301520.139237] SLOW spr round 5 (radius: 5)
[04:09:33 -301520.139035] SLOW spr round 6 (radius: 10)
[04:11:49 -301515.843250] SLOW spr round 7 (radius: 5)
[04:14:23 -301515.268551] SLOW spr round 8 (radius: 5)
[04:16:41 -301515.268442] SLOW spr round 9 (radius: 10)
[04:18:54 -301515.268435] SLOW spr round 10 (radius: 15)
[04:22:21 -301515.268433] SLOW spr round 11 (radius: 20)
[04:27:30 -301515.268431] SLOW spr round 12 (radius: 25)
[04:34:09 -301515.268429] Model parameter optimization (eps = 0.100000)

[04:34:12] ML tree search #4, logLikelihood: -301515.258374

[04:34:13 -802530.332313] Initial branch length optimization
[04:34:16 -685839.772765] Model parameter optimization (eps = 10.000000)
[04:34:52 -683708.262293] AUTODETECT spr round 1 (radius: 5)
[04:36:51 -520955.021120] AUTODETECT spr round 2 (radius: 10)
[04:39:08 -402562.336344] AUTODETECT spr round 3 (radius: 15)
[04:41:33 -350351.148152] AUTODETECT spr round 4 (radius: 20)
[04:44:23 -338014.957168] AUTODETECT spr round 5 (radius: 25)
[04:47:48 -335020.549757] SPR radius for FAST iterations: 25 (autodetect)
[04:47:48 -335020.549757] Model parameter optimization (eps = 3.000000)
[04:48:06 -334637.647066] FAST spr round 1 (radius: 25)
[04:51:29 -302452.815721] FAST spr round 2 (radius: 25)
[04:53:52 -301677.649380] FAST spr round 3 (radius: 25)
[04:55:57 -301622.631625] FAST spr round 4 (radius: 25)
[04:57:48 -301611.464635] FAST spr round 5 (radius: 25)
[04:59:36 -301596.538144] FAST spr round 6 (radius: 25)
[05:01:21 -301596.538133] Model parameter optimization (eps = 1.000000)
[05:01:36 -301593.507616] SLOW spr round 1 (radius: 5)
[05:04:00 -301541.701271] SLOW spr round 2 (radius: 5)
[05:06:14 -301540.645185] SLOW spr round 3 (radius: 5)
[05:08:25 -301540.644219] SLOW spr round 4 (radius: 10)
[05:10:44 -301539.605183] SLOW spr round 5 (radius: 5)
[05:13:20 -301539.604707] SLOW spr round 6 (radius: 10)
[05:15:52 -301539.604600] SLOW spr round 7 (radius: 15)
[05:19:25 -301535.492745] SLOW spr round 8 (radius: 5)
[05:22:10 -301533.696189] SLOW spr round 9 (radius: 5)
[05:24:35 -301533.695724] SLOW spr round 10 (radius: 10)
[05:26:59 -301533.695703] SLOW spr round 11 (radius: 15)
[05:30:37 -301533.695696] SLOW spr round 12 (radius: 20)
[05:35:55 -301533.695691] SLOW spr round 13 (radius: 25)
[05:43:01 -301533.695688] Model parameter optimization (eps = 0.100000)

[05:43:16] ML tree search #5, logLikelihood: -301531.678166

[05:43:16 -805585.101609] Initial branch length optimization
[05:43:19 -689119.142991] Model parameter optimization (eps = 10.000000)
[05:44:06 -686969.533998] AUTODETECT spr round 1 (radius: 5)
[05:46:08 -522242.015926] AUTODETECT spr round 2 (radius: 10)
[05:48:27 -407514.284114] AUTODETECT spr round 3 (radius: 15)
[05:50:54 -351842.165439] AUTODETECT spr round 4 (radius: 20)
[05:53:43 -333887.121071] AUTODETECT spr round 5 (radius: 25)
[05:57:16 -331508.360240] SPR radius for FAST iterations: 25 (autodetect)
[05:57:16 -331508.360240] Model parameter optimization (eps = 3.000000)
[05:57:35 -331211.372809] FAST spr round 1 (radius: 25)
[06:00:54 -302675.325500] FAST spr round 2 (radius: 25)
[06:03:10 -301789.348453] FAST spr round 3 (radius: 25)
[06:05:05 -301662.735721] FAST spr round 4 (radius: 25)
[06:06:47 -301653.093061] FAST spr round 5 (radius: 25)
[06:08:27 -301653.092009] Model parameter optimization (eps = 1.000000)
[06:08:32 -301653.084430] SLOW spr round 1 (radius: 5)
[06:10:49 -301565.335904] SLOW spr round 2 (radius: 5)
[06:13:01 -301559.546001] SLOW spr round 3 (radius: 5)
[06:15:03 -301559.541099] SLOW spr round 4 (radius: 10)
[06:17:10 -301557.112913] SLOW spr round 5 (radius: 5)
[06:19:34 -301557.112703] SLOW spr round 6 (radius: 10)
[06:22:01 -301557.112691] SLOW spr round 7 (radius: 15)
[06:25:25 -301553.968483] SLOW spr round 8 (radius: 5)
[06:28:06 -301553.253084] SLOW spr round 9 (radius: 5)
[06:30:29 -301553.251514] SLOW spr round 10 (radius: 10)
[06:32:48 -301553.251249] SLOW spr round 11 (radius: 15)
[06:36:20 -301553.251209] SLOW spr round 12 (radius: 20)
[06:41:24 -301553.251202] SLOW spr round 13 (radius: 25)
[06:47:48 -301553.251199] Model parameter optimization (eps = 0.100000)

[06:48:04] ML tree search #6, logLikelihood: -301546.567112

[06:48:04 -801701.558851] Initial branch length optimization
[06:48:08 -684305.195726] Model parameter optimization (eps = 10.000000)
[06:49:04 -682570.270728] AUTODETECT spr round 1 (radius: 5)
[06:51:05 -528589.384455] AUTODETECT spr round 2 (radius: 10)
[06:53:21 -411602.235670] AUTODETECT spr round 3 (radius: 15)
[06:55:55 -359609.311839] AUTODETECT spr round 4 (radius: 20)
[06:58:55 -336798.353556] AUTODETECT spr round 5 (radius: 25)
[07:02:36 -333238.376533] SPR radius for FAST iterations: 25 (autodetect)
[07:02:36 -333238.376533] Model parameter optimization (eps = 3.000000)
[07:02:56 -333035.401389] FAST spr round 1 (radius: 25)
[07:06:17 -302797.724558] FAST spr round 2 (radius: 25)
[07:08:43 -301704.974982] FAST spr round 3 (radius: 25)
[07:10:45 -301615.947498] FAST spr round 4 (radius: 25)
[07:12:34 -301603.662931] FAST spr round 5 (radius: 25)
[07:14:20 -301594.296711] FAST spr round 6 (radius: 25)
[07:16:04 -301594.296483] Model parameter optimization (eps = 1.000000)
[07:16:13 -301592.757050] SLOW spr round 1 (radius: 5)
[07:18:38 -301522.869003] SLOW spr round 2 (radius: 5)
[07:20:59 -301510.395246] SLOW spr round 3 (radius: 5)
[07:23:14 -301505.514217] SLOW spr round 4 (radius: 5)
[07:25:25 -301505.396205] SLOW spr round 5 (radius: 5)
[07:27:36 -301505.395275] SLOW spr round 6 (radius: 10)
[07:29:49 -301505.394727] SLOW spr round 7 (radius: 15)
[07:33:23 -301505.394252] SLOW spr round 8 (radius: 20)
[07:38:12 -301505.393836] SLOW spr round 9 (radius: 25)
[07:44:18 -301505.393470] Model parameter optimization (eps = 0.100000)

[07:44:22] ML tree search #7, logLikelihood: -301505.359987

[07:44:22 -803547.631436] Initial branch length optimization
[07:44:26 -687997.218140] Model parameter optimization (eps = 10.000000)
[07:45:02 -685954.315020] AUTODETECT spr round 1 (radius: 5)
[07:46:55 -513155.474299] AUTODETECT spr round 2 (radius: 10)
[07:49:01 -413743.631981] AUTODETECT spr round 3 (radius: 15)
[07:51:23 -360892.901571] AUTODETECT spr round 4 (radius: 20)
[07:54:10 -338074.333430] AUTODETECT spr round 5 (radius: 25)
[07:57:10 -335211.378253] SPR radius for FAST iterations: 25 (autodetect)
[07:57:10 -335211.378253] Model parameter optimization (eps = 3.000000)
[07:57:28 -334976.366506] FAST spr round 1 (radius: 25)
[08:00:40 -302566.139872] FAST spr round 2 (radius: 25)
[08:02:56 -301730.551815] FAST spr round 3 (radius: 25)
[08:04:53 -301687.163419] FAST spr round 4 (radius: 25)
[08:06:38 -301685.344880] FAST spr round 5 (radius: 25)
[08:08:18 -301684.291312] FAST spr round 6 (radius: 25)
[08:09:57 -301684.290559] Model parameter optimization (eps = 1.000000)
[08:10:11 -301680.322223] SLOW spr round 1 (radius: 5)
[08:12:28 -301613.952748] SLOW spr round 2 (radius: 5)
[08:14:39 -301599.450616] SLOW spr round 3 (radius: 5)
[08:16:46 -301597.276483] SLOW spr round 4 (radius: 5)
[08:18:51 -301597.276265] SLOW spr round 5 (radius: 10)
[08:21:01 -301596.562887] SLOW spr round 6 (radius: 5)
[08:23:31 -301595.391113] SLOW spr round 7 (radius: 5)
[08:25:47 -301595.390783] SLOW spr round 8 (radius: 10)
[08:28:02 -301595.363587] SLOW spr round 9 (radius: 15)
[08:31:36 -301595.363413] SLOW spr round 10 (radius: 20)
[08:36:56 -301595.363390] SLOW spr round 11 (radius: 25)
[08:43:41 -301595.363387] Model parameter optimization (eps = 0.100000)

[08:43:48] ML tree search #8, logLikelihood: -301595.214511

[08:43:48 -805188.086843] Initial branch length optimization
[08:43:52 -688915.873303] Model parameter optimization (eps = 10.000000)
[08:44:24 -686770.233148] AUTODETECT spr round 1 (radius: 5)
[08:46:14 -523084.500652] AUTODETECT spr round 2 (radius: 10)
[08:48:20 -401816.154126] AUTODETECT spr round 3 (radius: 15)
[08:50:41 -346399.004681] AUTODETECT spr round 4 (radius: 20)
[08:53:35 -332089.296207] AUTODETECT spr round 5 (radius: 25)
[08:56:45 -331255.459432] SPR radius for FAST iterations: 25 (autodetect)
[08:56:45 -331255.459432] Model parameter optimization (eps = 3.000000)
[08:57:07 -330975.200042] FAST spr round 1 (radius: 25)
[09:00:12 -303057.685517] FAST spr round 2 (radius: 25)
[09:02:26 -301841.919526] FAST spr round 3 (radius: 25)
[09:04:30 -301687.319885] FAST spr round 4 (radius: 25)
[09:06:18 -301613.499296] FAST spr round 5 (radius: 25)
[09:08:00 -301611.310899] FAST spr round 6 (radius: 25)
[09:09:38 -301611.309008] Model parameter optimization (eps = 1.000000)
[09:09:56 -301603.086879] SLOW spr round 1 (radius: 5)
[09:12:12 -301541.791859] SLOW spr round 2 (radius: 5)
[09:14:24 -301534.169030] SLOW spr round 3 (radius: 5)
[09:16:34 -301534.168755] SLOW spr round 4 (radius: 10)
[09:18:50 -301534.063524] SLOW spr round 5 (radius: 5)
[09:21:27 -301534.063155] SLOW spr round 6 (radius: 10)
[09:23:59 -301534.063120] SLOW spr round 7 (radius: 15)
[09:27:31 -301532.956384] SLOW spr round 8 (radius: 5)
[09:30:13 -301531.843215] SLOW spr round 9 (radius: 5)
[09:32:36 -301531.843206] SLOW spr round 10 (radius: 10)
[09:35:00 -301531.843204] SLOW spr round 11 (radius: 15)
[09:38:34 -301531.843203] SLOW spr round 12 (radius: 20)
[09:43:55 -301531.843201] SLOW spr round 13 (radius: 25)
[09:50:34 -301531.843200] Model parameter optimization (eps = 0.100000)

[09:50:40] ML tree search #9, logLikelihood: -301531.778354

[09:50:40 -804474.863234] Initial branch length optimization
[09:50:44 -689167.475900] Model parameter optimization (eps = 10.000000)
[09:51:32 -687176.542442] AUTODETECT spr round 1 (radius: 5)
[09:53:33 -522773.652656] AUTODETECT spr round 2 (radius: 10)
[09:55:51 -400130.799428] AUTODETECT spr round 3 (radius: 15)
[09:58:17 -346735.568146] AUTODETECT spr round 4 (radius: 20)
[10:00:51 -331275.808155] AUTODETECT spr round 5 (radius: 25)
[10:03:54 -330624.003647] SPR radius for FAST iterations: 25 (autodetect)
[10:03:54 -330624.003647] Model parameter optimization (eps = 3.000000)
[10:04:14 -330401.361648] FAST spr round 1 (radius: 25)
[10:07:22 -303779.544896] FAST spr round 2 (radius: 25)
[10:09:47 -301966.239897] FAST spr round 3 (radius: 25)
[10:12:02 -301679.983945] FAST spr round 4 (radius: 25)
[10:13:57 -301656.661359] FAST spr round 5 (radius: 25)
[10:15:45 -301655.755446] FAST spr round 6 (radius: 25)
[10:17:30 -301655.755172] Model parameter optimization (eps = 1.000000)
[10:17:45 -301647.561978] SLOW spr round 1 (radius: 5)
[10:20:09 -301573.418836] SLOW spr round 2 (radius: 5)
[10:22:26 -301565.681265] SLOW spr round 3 (radius: 5)
[10:24:41 -301545.213414] SLOW spr round 4 (radius: 5)
[10:26:46 -301539.592481] SLOW spr round 5 (radius: 5)
[10:28:48 -301539.591014] SLOW spr round 6 (radius: 10)
[10:31:02 -301528.919471] SLOW spr round 7 (radius: 5)
[10:33:33 -301527.212640] SLOW spr round 8 (radius: 5)
[10:35:48 -301527.212319] SLOW spr round 9 (radius: 10)
[10:38:03 -301526.931658] SLOW spr round 10 (radius: 5)
[10:40:34 -301520.598913] SLOW spr round 11 (radius: 5)
[10:42:54 -301520.107011] SLOW spr round 12 (radius: 5)
[10:45:08 -301520.106966] SLOW spr round 13 (radius: 10)
[10:47:25 -301520.106963] SLOW spr round 14 (radius: 15)
[10:51:02 -301520.106961] SLOW spr round 15 (radius: 20)
[10:56:08 -301520.106960] SLOW spr round 16 (radius: 25)
[11:02:28 -301520.106958] Model parameter optimization (eps = 0.100000)

[11:02:41] ML tree search #10, logLikelihood: -301518.827131

[11:02:41 -801833.098676] Initial branch length optimization
[11:02:45 -685132.256712] Model parameter optimization (eps = 10.000000)
[11:03:22 -683145.512689] AUTODETECT spr round 1 (radius: 5)
[11:05:23 -522660.966278] AUTODETECT spr round 2 (radius: 10)
[11:07:37 -408661.545717] AUTODETECT spr round 3 (radius: 15)
[11:10:08 -362750.706869] AUTODETECT spr round 4 (radius: 20)
[11:13:06 -337424.562981] AUTODETECT spr round 5 (radius: 25)
[11:16:39 -335897.754780] SPR radius for FAST iterations: 25 (autodetect)
[11:16:40 -335897.754780] Model parameter optimization (eps = 3.000000)
[11:16:45 -335897.384809] FAST spr round 1 (radius: 25)
[11:20:03 -303249.697769] FAST spr round 2 (radius: 25)
[11:22:24 -301946.014563] FAST spr round 3 (radius: 25)
[11:24:26 -301873.300602] FAST spr round 4 (radius: 25)
[11:26:15 -301868.261616] FAST spr round 5 (radius: 25)
[11:27:59 -301866.513386] FAST spr round 6 (radius: 25)
[11:29:43 -301866.513162] Model parameter optimization (eps = 1.000000)
[11:29:47 -301866.499463] SLOW spr round 1 (radius: 5)
[11:32:05 -301767.825324] SLOW spr round 2 (radius: 5)
[11:34:17 -301758.196289] SLOW spr round 3 (radius: 5)
[11:36:25 -301758.195072] SLOW spr round 4 (radius: 10)
[11:38:37 -301757.447324] SLOW spr round 5 (radius: 5)
[11:41:10 -301741.904737] SLOW spr round 6 (radius: 5)
[11:43:28 -301739.936412] SLOW spr round 7 (radius: 5)
[11:45:38 -301739.935838] SLOW spr round 8 (radius: 10)
[11:47:51 -301739.935629] SLOW spr round 9 (radius: 15)
[11:51:18 -301739.070963] SLOW spr round 10 (radius: 5)
[11:53:51 -301737.149346] SLOW spr round 11 (radius: 5)
[11:56:05 -301736.285051] SLOW spr round 12 (radius: 5)
[11:58:09 -301736.283428] SLOW spr round 13 (radius: 10)
[12:00:18 -301736.098230] SLOW spr round 14 (radius: 5)
[12:02:44 -301736.097823] SLOW spr round 15 (radius: 10)
[12:05:04 -301736.097632] SLOW spr round 16 (radius: 15)
[12:08:15 -301736.097445] SLOW spr round 17 (radius: 20)
[12:13:18 -301736.097258] SLOW spr round 18 (radius: 25)
[12:19:46 -301736.097070] Model parameter optimization (eps = 0.100000)

[12:20:13] ML tree search #11, logLikelihood: -301532.109402

[12:20:13 -805853.300468] Initial branch length optimization
[12:20:18 -688432.188242] Model parameter optimization (eps = 10.000000)
[12:20:59 -686188.084389] AUTODETECT spr round 1 (radius: 5)
[12:22:59 -522691.065125] AUTODETECT spr round 2 (radius: 10)
[12:25:17 -396854.352949] AUTODETECT spr round 3 (radius: 15)
[12:27:38 -357193.953281] AUTODETECT spr round 4 (radius: 20)
[12:30:22 -336370.993536] AUTODETECT spr round 5 (radius: 25)
[12:33:31 -335187.493951] SPR radius for FAST iterations: 25 (autodetect)
[12:33:31 -335187.493951] Model parameter optimization (eps = 3.000000)
[12:33:36 -335186.939580] FAST spr round 1 (radius: 25)
[12:36:46 -303203.279259] FAST spr round 2 (radius: 25)
[12:39:09 -302081.960024] FAST spr round 3 (radius: 25)
[12:41:13 -301899.483221] FAST spr round 4 (radius: 25)
[12:43:02 -301895.195500] FAST spr round 5 (radius: 25)
[12:44:47 -301895.193410] Model parameter optimization (eps = 1.000000)
[12:45:08 -301679.902742] SLOW spr round 1 (radius: 5)
[12:47:32 -301562.661280] SLOW spr round 2 (radius: 5)
[12:49:52 -301541.942910] SLOW spr round 3 (radius: 5)
[12:52:06 -301538.115173] SLOW spr round 4 (radius: 5)
[12:54:16 -301538.114804] SLOW spr round 5 (radius: 10)
[12:56:34 -301525.879261] SLOW spr round 6 (radius: 5)
[12:59:14 -301519.040751] SLOW spr round 7 (radius: 5)
[13:01:35 -301518.734791] SLOW spr round 8 (radius: 5)
[13:03:48 -301518.733727] SLOW spr round 9 (radius: 10)
[13:06:05 -301518.733643] SLOW spr round 10 (radius: 15)
[13:09:37 -301518.733617] SLOW spr round 11 (radius: 20)
[13:14:35 -301518.733596] SLOW spr round 12 (radius: 25)
[13:20:58 -301518.733576] Model parameter optimization (eps = 0.100000)

[13:21:19] ML tree search #12, logLikelihood: -301515.672897

[13:21:20 -802227.991052] Initial branch length optimization
[13:21:24 -685613.353188] Model parameter optimization (eps = 10.000000)
[13:22:12 -683405.166484] AUTODETECT spr round 1 (radius: 5)
[13:24:14 -524923.063564] AUTODETECT spr round 2 (radius: 10)
[13:26:28 -414668.327382] AUTODETECT spr round 3 (radius: 15)
[13:28:58 -345082.300363] AUTODETECT spr round 4 (radius: 20)
[13:31:46 -332045.557661] AUTODETECT spr round 5 (radius: 25)
[13:34:51 -330313.298530] SPR radius for FAST iterations: 25 (autodetect)
[13:34:51 -330313.298530] Model parameter optimization (eps = 3.000000)
[13:35:09 -330045.897210] FAST spr round 1 (radius: 25)
[13:38:15 -303329.299605] FAST spr round 2 (radius: 25)
[13:40:33 -301887.926623] FAST spr round 3 (radius: 25)
[13:42:34 -301744.851306] FAST spr round 4 (radius: 25)
[13:44:22 -301703.125156] FAST spr round 5 (radius: 25)
[13:46:01 -301700.157417] FAST spr round 6 (radius: 25)
[13:47:39 -301700.156689] Model parameter optimization (eps = 1.000000)
[13:47:52 -301689.838705] SLOW spr round 1 (radius: 5)
[13:50:13 -301596.490102] SLOW spr round 2 (radius: 5)
[13:52:31 -301581.422882] SLOW spr round 3 (radius: 5)
[13:54:41 -301581.418247] SLOW spr round 4 (radius: 10)
[13:56:57 -301565.100992] SLOW spr round 5 (radius: 5)
[13:59:33 -301554.974814] SLOW spr round 6 (radius: 5)
[14:01:54 -301554.600252] SLOW spr round 7 (radius: 5)
[14:04:08 -301553.040301] SLOW spr round 8 (radius: 5)
[14:06:17 -301553.038192] SLOW spr round 9 (radius: 10)
[14:08:31 -301551.436922] SLOW spr round 10 (radius: 5)
[14:11:04 -301542.003317] SLOW spr round 11 (radius: 5)
[14:13:22 -301542.003041] SLOW spr round 12 (radius: 10)
[14:15:40 -301541.142350] SLOW spr round 13 (radius: 5)
[14:18:12 -301541.069016] SLOW spr round 14 (radius: 10)
[14:20:39 -301541.068619] SLOW spr round 15 (radius: 15)
[14:23:58 -301541.068384] SLOW spr round 16 (radius: 20)
[14:29:04 -301541.068184] SLOW spr round 17 (radius: 25)
[14:35:22 -301541.067992] Model parameter optimization (eps = 0.100000)

[14:35:26] ML tree search #13, logLikelihood: -301541.064949

[14:35:26 -798995.458168] Initial branch length optimization
[14:35:30 -684974.334444] Model parameter optimization (eps = 10.000000)
[14:36:17 -682844.151290] AUTODETECT spr round 1 (radius: 5)
[14:38:15 -527841.157039] AUTODETECT spr round 2 (radius: 10)
[14:40:35 -410375.417457] AUTODETECT spr round 3 (radius: 15)
[14:43:04 -346651.091520] AUTODETECT spr round 4 (radius: 20)
[14:45:55 -334421.869795] AUTODETECT spr round 5 (radius: 25)
[14:49:05 -330188.515127] SPR radius for FAST iterations: 25 (autodetect)
[14:49:05 -330188.515127] Model parameter optimization (eps = 3.000000)
[14:49:12 -330169.538269] FAST spr round 1 (radius: 25)
[14:52:20 -303822.860557] FAST spr round 2 (radius: 25)
[14:54:44 -302077.437792] FAST spr round 3 (radius: 25)
[14:56:50 -301909.640952] FAST spr round 4 (radius: 25)
[14:58:39 -301905.152149] FAST spr round 5 (radius: 25)
[15:00:26 -301905.151544] Model parameter optimization (eps = 1.000000)
[15:00:31 -301904.881872] SLOW spr round 1 (radius: 5)
[15:02:55 -301831.001607] SLOW spr round 2 (radius: 5)
[15:05:10 -301817.219305] SLOW spr round 3 (radius: 5)
[15:07:17 -301815.968559] SLOW spr round 4 (radius: 5)
[15:09:19 -301815.968141] SLOW spr round 5 (radius: 10)
[15:11:27 -301808.726788] SLOW spr round 6 (radius: 5)
[15:13:49 -301800.731180] SLOW spr round 7 (radius: 5)
[15:15:59 -301800.730804] SLOW spr round 8 (radius: 10)
[15:18:07 -301800.730608] SLOW spr round 9 (radius: 15)
[15:21:20 -301800.730431] SLOW spr round 10 (radius: 20)
[15:26:18 -301800.730258] SLOW spr round 11 (radius: 25)
[15:32:48 -301800.730084] Model parameter optimization (eps = 0.100000)

[15:32:52] ML tree search #14, logLikelihood: -301800.716245

[15:32:52 -804594.941821] Initial branch length optimization
[15:32:56 -685249.421382] Model parameter optimization (eps = 10.000000)
[15:33:36 -683262.937877] AUTODETECT spr round 1 (radius: 5)
[15:35:33 -526180.860726] AUTODETECT spr round 2 (radius: 10)
[15:37:48 -407766.037218] AUTODETECT spr round 3 (radius: 15)
[15:40:16 -359490.794978] AUTODETECT spr round 4 (radius: 20)
[15:43:02 -346732.349888] AUTODETECT spr round 5 (radius: 25)
[15:46:28 -334015.060561] SPR radius for FAST iterations: 25 (autodetect)
[15:46:28 -334015.060561] Model parameter optimization (eps = 3.000000)
[15:46:33 -334014.810427] FAST spr round 1 (radius: 25)
[15:50:00 -303031.541916] FAST spr round 2 (radius: 25)
[15:52:21 -301910.509755] FAST spr round 3 (radius: 25)
[15:54:25 -301848.742906] FAST spr round 4 (radius: 25)
[15:56:13 -301835.584593] FAST spr round 5 (radius: 25)
[15:57:57 -301832.362218] FAST spr round 6 (radius: 25)
[15:59:38 -301832.362195] Model parameter optimization (eps = 1.000000)
[15:59:43 -301832.283915] SLOW spr round 1 (radius: 5)
[16:02:06 -301736.048954] SLOW spr round 2 (radius: 5)
[16:04:21 -301724.359636] SLOW spr round 3 (radius: 5)
[16:06:29 -301724.125840] SLOW spr round 4 (radius: 5)
[16:08:36 -301724.125716] SLOW spr round 5 (radius: 10)
[16:10:47 -301718.578280] SLOW spr round 6 (radius: 5)
[16:13:15 -301716.171288] SLOW spr round 7 (radius: 5)
[16:15:25 -301716.171197] SLOW spr round 8 (radius: 10)
[16:17:34 -301715.626786] SLOW spr round 9 (radius: 5)
[16:19:55 -301714.887936] SLOW spr round 10 (radius: 5)
[16:22:01 -301714.887934] SLOW spr round 11 (radius: 10)
[16:24:10 -301714.887932] SLOW spr round 12 (radius: 15)
[16:27:30 -301714.887931] SLOW spr round 13 (radius: 20)
[16:32:23 -301714.887929] SLOW spr round 14 (radius: 25)
[16:38:18 -301714.887928] Model parameter optimization (eps = 0.100000)

[16:38:21] ML tree search #15, logLikelihood: -301714.886259

[16:38:21 -806641.760996] Initial branch length optimization
[16:38:25 -691385.170112] Model parameter optimization (eps = 10.000000)
[16:39:08 -689220.800655] AUTODETECT spr round 1 (radius: 5)
[16:41:04 -531415.902695] AUTODETECT spr round 2 (radius: 10)
[16:43:21 -410678.666410] AUTODETECT spr round 3 (radius: 15)
[16:45:47 -363528.365997] AUTODETECT spr round 4 (radius: 20)
[16:48:35 -340664.452185] AUTODETECT spr round 5 (radius: 25)
[16:51:47 -337585.817702] SPR radius for FAST iterations: 25 (autodetect)
[16:51:47 -337585.817702] Model parameter optimization (eps = 3.000000)
[16:52:10 -337337.839538] FAST spr round 1 (radius: 25)
[16:55:31 -302895.662270] FAST spr round 2 (radius: 25)
[16:57:52 -301783.355321] FAST spr round 3 (radius: 25)
[17:00:00 -301680.721726] FAST spr round 4 (radius: 25)
[17:01:57 -301656.340614] FAST spr round 5 (radius: 25)
[17:03:49 -301646.766678] FAST spr round 6 (radius: 25)
[17:05:35 -301643.498622] FAST spr round 7 (radius: 25)
[17:07:17 -301643.498583] Model parameter optimization (eps = 1.000000)
[17:07:33 -301639.884611] SLOW spr round 1 (radius: 5)
[17:09:55 -301557.561814] SLOW spr round 2 (radius: 5)
[17:12:15 -301535.981599] SLOW spr round 3 (radius: 5)
[17:14:31 -301524.880067] SLOW spr round 4 (radius: 5)
[17:16:41 -301524.208580] SLOW spr round 5 (radius: 5)
[17:18:50 -301524.208190] SLOW spr round 6 (radius: 10)
[17:21:07 -301522.204751] SLOW spr round 7 (radius: 5)
[17:23:42 -301521.678081] SLOW spr round 8 (radius: 5)
[17:26:02 -301521.678015] SLOW spr round 9 (radius: 10)
[17:28:23 -301521.677993] SLOW spr round 10 (radius: 15)
[17:31:53 -301521.677972] SLOW spr round 11 (radius: 20)
[17:36:50 -301521.677951] SLOW spr round 12 (radius: 25)
[17:43:14 -301521.677931] Model parameter optimization (eps = 0.100000)

[17:43:23] ML tree search #16, logLikelihood: -301521.382203

[17:43:24 -805139.548702] Initial branch length optimization
[17:43:28 -689113.745274] Model parameter optimization (eps = 10.000000)
[17:44:07 -687156.312491] AUTODETECT spr round 1 (radius: 5)
[17:46:08 -523241.672927] AUTODETECT spr round 2 (radius: 10)
[17:48:27 -406731.822139] AUTODETECT spr round 3 (radius: 15)
[17:50:58 -352660.705141] AUTODETECT spr round 4 (radius: 20)
[17:53:49 -337585.222882] AUTODETECT spr round 5 (radius: 25)
[17:57:02 -333432.953737] SPR radius for FAST iterations: 25 (autodetect)
[17:57:03 -333432.953737] Model parameter optimization (eps = 3.000000)
[17:57:08 -333431.571087] FAST spr round 1 (radius: 25)
[18:00:25 -303518.627194] FAST spr round 2 (radius: 25)
[18:02:49 -302211.956724] FAST spr round 3 (radius: 25)
[18:04:45 -301929.954922] FAST spr round 4 (radius: 25)
[18:06:33 -301895.810719] FAST spr round 5 (radius: 25)
[18:08:10 -301895.810459] Model parameter optimization (eps = 1.000000)
[18:08:15 -301895.483593] SLOW spr round 1 (radius: 5)
[18:10:28 -301810.759083] SLOW spr round 2 (radius: 5)
[18:12:37 -301793.128518] SLOW spr round 3 (radius: 5)
[18:14:41 -301791.833720] SLOW spr round 4 (radius: 5)
[18:16:40 -301791.833520] SLOW spr round 5 (radius: 10)
[18:18:46 -301784.185801] SLOW spr round 6 (radius: 5)
[18:21:08 -301782.581799] SLOW spr round 7 (radius: 5)
[18:23:23 -301782.580174] SLOW spr round 8 (radius: 10)
[18:25:36 -301782.580122] SLOW spr round 9 (radius: 15)
[18:28:58 -301778.775230] SLOW spr round 10 (radius: 5)
[18:31:32 -301778.187437] SLOW spr round 11 (radius: 5)
[18:33:51 -301778.187412] SLOW spr round 12 (radius: 10)
[18:36:05 -301778.187410] SLOW spr round 13 (radius: 15)
[18:39:24 -301778.187409] SLOW spr round 14 (radius: 20)
[18:44:14 -301778.187408] SLOW spr round 15 (radius: 25)
[18:50:20 -301778.187407] Model parameter optimization (eps = 0.100000)

[18:50:48] ML tree search #17, logLikelihood: -301561.617976

[18:50:49 -804446.891977] Initial branch length optimization
[18:50:52 -687820.587183] Model parameter optimization (eps = 10.000000)
[18:51:41 -685997.298113] AUTODETECT spr round 1 (radius: 5)
[18:53:39 -529845.769766] AUTODETECT spr round 2 (radius: 10)
[18:55:55 -413339.040794] AUTODETECT spr round 3 (radius: 15)
[18:58:21 -346341.819899] AUTODETECT spr round 4 (radius: 20)
[19:01:19 -335922.659055] AUTODETECT spr round 5 (radius: 25)
[19:04:42 -333086.620513] SPR radius for FAST iterations: 25 (autodetect)
[19:04:42 -333086.620513] Model parameter optimization (eps = 3.000000)
[19:04:47 -333085.701647] FAST spr round 1 (radius: 25)
[19:07:49 -303176.538364] FAST spr round 2 (radius: 25)
[19:10:06 -301977.823347] FAST spr round 3 (radius: 25)
[19:12:06 -301919.061684] FAST spr round 4 (radius: 25)
[19:13:54 -301915.071490] FAST spr round 5 (radius: 25)
[19:15:37 -301915.071132] Model parameter optimization (eps = 1.000000)
[19:15:57 -301637.564848] SLOW spr round 1 (radius: 5)
[19:18:18 -301524.236563] SLOW spr round 2 (radius: 5)
[19:20:35 -301518.888433] SLOW spr round 3 (radius: 5)
[19:22:46 -301517.787199] SLOW spr round 4 (radius: 5)
[19:24:57 -301516.783762] SLOW spr round 5 (radius: 5)
[19:27:06 -301516.783084] SLOW spr round 6 (radius: 10)
[19:29:22 -301511.936829] SLOW spr round 7 (radius: 5)
[19:31:57 -301511.410635] SLOW spr round 8 (radius: 5)
[19:34:14 -301511.410210] SLOW spr round 9 (radius: 10)
[19:36:30 -301511.410127] SLOW spr round 10 (radius: 15)
[19:39:51 -301511.410112] SLOW spr round 11 (radius: 20)
[19:44:42 -301511.410108] SLOW spr round 12 (radius: 25)
[19:50:56 -301511.410107] Model parameter optimization (eps = 0.100000)

[19:51:04] ML tree search #18, logLikelihood: -301510.985517

[19:51:04 -800485.775474] Initial branch length optimization
[19:51:08 -684156.491101] Model parameter optimization (eps = 10.000000)
[19:51:49 -682349.693274] AUTODETECT spr round 1 (radius: 5)
[19:53:42 -523408.919283] AUTODETECT spr round 2 (radius: 10)
[19:55:57 -419595.178008] AUTODETECT spr round 3 (radius: 15)
[19:58:24 -357949.501958] AUTODETECT spr round 4 (radius: 20)
[20:01:18 -334434.919950] AUTODETECT spr round 5 (radius: 25)
[20:04:40 -332406.421126] SPR radius for FAST iterations: 25 (autodetect)
[20:04:40 -332406.421126] Model parameter optimization (eps = 3.000000)
[20:04:57 -332221.927563] FAST spr round 1 (radius: 25)
[20:08:20 -303310.809989] FAST spr round 2 (radius: 25)
[20:10:43 -301794.692405] FAST spr round 3 (radius: 25)
[20:12:52 -301684.149649] FAST spr round 4 (radius: 25)
[20:14:41 -301673.068583] FAST spr round 5 (radius: 25)
[20:16:26 -301671.950888] FAST spr round 6 (radius: 25)
[20:18:13 -301666.520222] FAST spr round 7 (radius: 25)
[20:19:55 -301666.519502] Model parameter optimization (eps = 1.000000)
[20:20:13 -301659.675861] SLOW spr round 1 (radius: 5)
[20:22:37 -301569.461596] SLOW spr round 2 (radius: 5)
[20:24:54 -301558.338531] SLOW spr round 3 (radius: 5)
[20:27:05 -301558.128254] SLOW spr round 4 (radius: 5)
[20:29:14 -301558.127946] SLOW spr round 5 (radius: 10)
[20:31:30 -301545.757011] SLOW spr round 6 (radius: 5)
[20:34:07 -301531.930033] SLOW spr round 7 (radius: 5)
[20:36:25 -301531.929681] SLOW spr round 8 (radius: 10)
[20:38:42 -301531.718353] SLOW spr round 9 (radius: 5)
[20:41:15 -301530.968040] SLOW spr round 10 (radius: 5)
[20:43:31 -301530.967654] SLOW spr round 11 (radius: 10)
[20:45:50 -301528.332195] SLOW spr round 12 (radius: 5)
[20:48:24 -301526.877405] SLOW spr round 13 (radius: 5)
[20:50:42 -301526.378879] SLOW spr round 14 (radius: 5)
[20:52:54 -301526.378607] SLOW spr round 15 (radius: 10)
[20:55:08 -301526.378584] SLOW spr round 16 (radius: 15)
[20:58:41 -301526.378580] SLOW spr round 17 (radius: 20)
[21:03:31 -301526.378578] SLOW spr round 18 (radius: 25)
[21:09:40 -301526.378576] Model parameter optimization (eps = 0.100000)

[21:09:53] ML tree search #19, logLikelihood: -301525.925671

[21:09:53 -809329.352250] Initial branch length optimization
[21:09:57 -692806.588743] Model parameter optimization (eps = 10.000000)
[21:10:34 -690542.588755] AUTODETECT spr round 1 (radius: 5)
[21:12:28 -526340.977743] AUTODETECT spr round 2 (radius: 10)
[21:14:37 -415114.659270] AUTODETECT spr round 3 (radius: 15)
[21:16:58 -361448.893897] AUTODETECT spr round 4 (radius: 20)
[21:19:39 -343310.823502] AUTODETECT spr round 5 (radius: 25)
[21:22:35 -338849.493425] SPR radius for FAST iterations: 25 (autodetect)
[21:22:35 -338849.493425] Model parameter optimization (eps = 3.000000)
[21:22:42 -338844.400607] FAST spr round 1 (radius: 25)
[21:25:41 -304638.556609] FAST spr round 2 (radius: 25)
[21:27:57 -302899.704712] FAST spr round 3 (radius: 25)
[21:29:58 -302224.195763] FAST spr round 4 (radius: 25)
[21:31:53 -301931.421308] FAST spr round 5 (radius: 25)
[21:33:40 -301914.262408] FAST spr round 6 (radius: 25)
[21:35:23 -301899.217152] FAST spr round 7 (radius: 25)
[21:37:05 -301899.217005] Model parameter optimization (eps = 1.000000)
[21:37:26 -301681.009181] SLOW spr round 1 (radius: 5)
[21:39:46 -301590.275555] SLOW spr round 2 (radius: 5)
[21:41:58 -301586.849276] SLOW spr round 3 (radius: 5)
[21:44:06 -301586.366509] SLOW spr round 4 (radius: 5)
[21:46:14 -301586.366496] SLOW spr round 5 (radius: 10)
[21:48:29 -301581.137557] SLOW spr round 6 (radius: 5)
[21:51:07 -301569.816120] SLOW spr round 7 (radius: 5)
[21:53:27 -301567.701089] SLOW spr round 8 (radius: 5)
[21:55:38 -301567.700968] SLOW spr round 9 (radius: 10)
[21:57:55 -301565.999045] SLOW spr round 10 (radius: 5)
[22:00:28 -301565.968296] SLOW spr round 11 (radius: 10)
[22:02:57 -301564.883597] SLOW spr round 12 (radius: 5)
[22:05:27 -301564.883227] SLOW spr round 13 (radius: 10)
[22:07:54 -301564.883222] SLOW spr round 14 (radius: 15)
[22:11:21 -301564.883220] SLOW spr round 15 (radius: 20)
[22:16:41 -301564.883219] SLOW spr round 16 (radius: 25)
[22:23:36 -301564.883217] Model parameter optimization (eps = 0.100000)

[22:23:51] ML tree search #20, logLikelihood: -301564.601198


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.165219,0.268695) (0.286693,0.382828) (0.328422,1.169192) (0.219667,2.102570) 
   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: -301503.965621

AIC score: 607017.931243 / AICc score: 8651077.931243 / BIC score: 615423.618034
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=489).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 37 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q2TAA5/3_mltree/Q2TAA5.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q2TAA5/3_mltree/Q2TAA5.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q2TAA5/3_mltree/Q2TAA5.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q2TAA5/3_mltree/Q2TAA5.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q2TAA5/3_mltree/Q2TAA5.raxml.log

Analysis started: 03-Jul-2021 18:05:49 / finished: 04-Jul-2021 16:29:40

Elapsed time: 80631.681 seconds

Consumed energy: 7154.062 Wh (= 36 km in an electric car, or 179 km with an e-scooter!)