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 05-Jul-2021 17:40:31 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A1L4H1/2_msa/A1L4H1_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A1L4H1/3_mltree/A1L4H1 --seed 2 --threads 3 --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 (3 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A1L4H1/2_msa/A1L4H1_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1000 taxa and 164 sites

WARNING: Sequences tr_A0A2R8QAP7_A0A2R8QAP7_DANRE_7955 and tr_F1QM24_F1QM24_DANRE_7955 are exactly identical!
WARNING: Sequences tr_G1QZT7_G1QZT7_NOMLE_61853 and tr_A0A1D5Q5F6_A0A1D5Q5F6_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G1QZT7_G1QZT7_NOMLE_61853 and tr_G7PCC1_G7PCC1_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G1QZT7_G1QZT7_NOMLE_61853 and tr_A0A096MYD3_A0A096MYD3_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G1QZT7_G1QZT7_NOMLE_61853 and tr_A0A0D9RBT1_A0A0D9RBT1_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G1QZT7_G1QZT7_NOMLE_61853 and tr_A0A2K5MHZ7_A0A2K5MHZ7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1QZT7_G1QZT7_NOMLE_61853 and tr_A0A2K6BTA1_A0A2K6BTA1_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G1QZT7_G1QZT7_NOMLE_61853 and tr_A0A2K6ABX7_A0A2K6ABX7_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G3QK11_G3QK11_GORGO_9595 and sp_Q5G270_NETR_GORGO_9595 are exactly identical!
WARNING: Sequences tr_G3QK11_G3QK11_GORGO_9595 and sp_P56730_NETR_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QK11_G3QK11_GORGO_9595 and tr_A0A2R9B643_A0A2R9B643_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3R058_G3R058_GORGO_9595 and sp_O43866_CD5L_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3R058_G3R058_GORGO_9595 and tr_A0A2R9CA56_A0A2R9CA56_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F1PL60_F1PL60_CANLF_9615 and sp_Q2VLG6_C163A_CANLF_9615 are exactly identical!
WARNING: Sequences tr_A0A2I3S5D8_A0A2I3S5D8_PANTR_9598 and sp_A1L4H1_SRCRL_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I3S5D8_A0A2I3S5D8_PANTR_9598 and tr_A0A2R8ZZ29_A0A2R8ZZ29_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2I3TAV9_A0A2I3TAV9_PANTR_9598 and tr_A0A2R9B9G2_A0A2R9B9G2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2R1S1_H2R1S1_PANTR_9598 and sp_Q9UGM3_DMBT1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2R1S1_H2R1S1_PANTR_9598 and tr_A0A2R9A5Z0_A0A2R9A5Z0_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2R585_H2R585_PANTR_9598 and sp_Q8WTU2_SRB4D_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2R585_H2R585_PANTR_9598 and tr_A0A2R8Z9H9_A0A2R8Z9H9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A1D5RG52_A0A1D5RG52_MACMU_9544 and tr_A0A2I3LS56_A0A2I3LS56_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5RG52_A0A1D5RG52_MACMU_9544 and tr_A0A2K5LH06_A0A2K5LH06_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5RG52_A0A1D5RG52_MACMU_9544 and tr_A0A2K6DH39_A0A2K6DH39_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7DZF6_F7DZF6_MACMU_9544 and sp_Q5G267_NETR_MACMU_9544 are exactly identical!
WARNING: Sequences tr_F7DZF6_F7DZF6_MACMU_9544 and tr_G7P658_G7P658_MACFA_9541 are exactly identical!
WARNING: Sequences tr_W4Z1U1_W4Z1U1_STRPU_7668 and tr_W4Z371_W4Z371_STRPU_7668 are exactly identical!
WARNING: Sequences tr_A0A287B9P2_A0A287B9P2_PIG_9823 and sp_Q2VL90_C163A_PIG_9823 are exactly identical!
WARNING: Sequences tr_B3S7M3_B3S7M3_TRIAD_10228 and tr_A0A369SPY2_A0A369SPY2_9METZ_287889 are exactly identical!
WARNING: Sequences tr_B3SC98_B3SC98_TRIAD_10228 and tr_A0A369S853_A0A369S853_9METZ_287889 are exactly identical!
WARNING: Sequences tr_B3SCU9_B3SCU9_TRIAD_10228 and tr_A0A369S493_A0A369S493_9METZ_287889 are exactly identical!
WARNING: Sequences tr_G7PCC0_G7PCC0_MACFA_9541 and tr_A0A2K6DLA6_A0A2K6DLA6_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096MYS3_A0A096MYS3_PAPAN_9555 and tr_A0A0D9RZV5_A0A0D9RZV5_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A096MYS3_A0A096MYS3_PAPAN_9555 and tr_A0A2K5N5Y7_A0A2K5N5Y7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096MYS3_A0A096MYS3_PAPAN_9555 and tr_A0A2K6BZ33_A0A2K6BZ33_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096NZ32_A0A096NZ32_PAPAN_9555 and tr_A0A0D9QUU7_A0A0D9QUU7_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A096NZ32_A0A096NZ32_PAPAN_9555 and tr_A0A2K5NTH6_A0A2K5NTH6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096NZ32_A0A096NZ32_PAPAN_9555 and tr_A0A2K6E0I0_A0A2K6E0I0_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096NZ32_A0A096NZ32_PAPAN_9555 and tr_A0A2K5YRZ9_A0A2K5YRZ9_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A226NAY3_A0A226NAY3_CALSU_9009 and tr_A0A226PFL0_A0A226PFL0_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A226NHH3_A0A226NHH3_CALSU_9009 and tr_A0A226PDB2_A0A226PDB2_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0QER9_A0A2D0QER9_ICTPU_7998 and tr_A0A2D0QFT7_A0A2D0QFT7_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0QLA3_A0A2D0QLA3_ICTPU_7998 and tr_A0A2D0QNN4_A0A2D0QNN4_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U4AR37_A0A2U4AR37_TURTR_9739 and tr_A0A2Y9Q3B4_A0A2Y9Q3B4_DELLE_9749 are exactly identical!
WARNING: Duplicate sequences found: 44

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/A1L4H1/3_mltree/A1L4H1.raxml.reduced.phy

Alignment comprises 1 partitions and 164 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 164 / 164
Gaps: 11.56 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A1L4H1/3_mltree/A1L4H1.raxml.rba

Parallelization scheme autoconfig: 3 worker(s) x 1 thread(s)

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

[00:00:00] Generating 20 random starting tree(s) with 1000 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 164 / 13120
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -226683.944971] Initial branch length optimization
[00:00:02 -198728.877228] Model parameter optimization (eps = 10.000000)
[00:00:44 -198480.933454] AUTODETECT spr round 1 (radius: 5)
[00:03:10 -159898.808636] AUTODETECT spr round 2 (radius: 10)
[00:05:58 -129418.485319] AUTODETECT spr round 3 (radius: 15)
[00:09:05 -115829.872277] AUTODETECT spr round 4 (radius: 20)
[00:12:41 -109076.185016] AUTODETECT spr round 5 (radius: 25)
[00:16:56 -104989.825354] SPR radius for FAST iterations: 25 (autodetect)
[00:16:56 -104989.825354] Model parameter optimization (eps = 3.000000)
[00:17:20 -104892.478196] FAST spr round 1 (radius: 25)
[00:22:34 -94615.045684] FAST spr round 2 (radius: 25)
[00:25:52 -93772.648359] FAST spr round 3 (radius: 25)
[00:28:31 -93633.868698] FAST spr round 4 (radius: 25)
[00:30:51 -93604.101891] FAST spr round 5 (radius: 25)
[00:32:58 -93599.619963] FAST spr round 6 (radius: 25)
[00:34:59 -93597.880165] FAST spr round 7 (radius: 25)
[00:36:56 -93597.802097] Model parameter optimization (eps = 1.000000)
[00:37:07 -93595.005222] SLOW spr round 1 (radius: 5)
[00:39:45 -93562.724111] SLOW spr round 2 (radius: 5)
[00:42:15 -93557.367824] SLOW spr round 3 (radius: 5)
[00:44:43 -93557.217108] SLOW spr round 4 (radius: 5)
[00:47:06 -93557.216867] SLOW spr round 5 (radius: 10)
[00:49:32 -93553.960405] SLOW spr round 6 (radius: 5)
[00:52:22 -93548.612302] SLOW spr round 7 (radius: 5)
[00:54:58 -93548.388771] SLOW spr round 8 (radius: 5)
[00:57:25 -93548.388752] SLOW spr round 9 (radius: 10)
[00:59:51 -93548.388752] SLOW spr round 10 (radius: 15)
[01:04:13 -93546.339831] SLOW spr round 11 (radius: 5)
[01:07:07 -93544.536185] SLOW spr round 12 (radius: 5)
[01:09:44 -93543.991547] SLOW spr round 13 (radius: 5)
[01:12:12 -93543.991462] SLOW spr round 14 (radius: 10)
[01:14:40 -93542.751796] SLOW spr round 15 (radius: 5)
[01:17:26 -93542.748493] SLOW spr round 16 (radius: 10)
[01:20:09 -93542.747955] SLOW spr round 17 (radius: 15)
[01:24:15 -93542.747845] SLOW spr round 18 (radius: 20)
[01:30:20 -93542.015728] SLOW spr round 19 (radius: 5)
[01:33:20 -93530.659174] SLOW spr round 20 (radius: 5)
[01:35:59 -93530.344034] SLOW spr round 21 (radius: 5)
[01:38:27 -93530.343677] SLOW spr round 22 (radius: 10)
[01:40:52 -93530.343653] SLOW spr round 23 (radius: 15)
[01:45:03 -93529.937286] SLOW spr round 24 (radius: 5)
[01:47:55 -93527.779904] SLOW spr round 25 (radius: 5)
[01:50:29 -93527.779752] SLOW spr round 26 (radius: 10)
[01:53:02 -93522.692384] SLOW spr round 27 (radius: 5)
[01:55:53 -93517.848584] SLOW spr round 28 (radius: 5)
[01:58:27 -93517.406743] SLOW spr round 29 (radius: 5)
[02:00:51 -93517.406596] SLOW spr round 30 (radius: 10)
[02:03:14 -93517.406593] SLOW spr round 31 (radius: 15)
[02:07:27 -93517.058390] SLOW spr round 32 (radius: 5)
[02:10:19 -93515.804190] SLOW spr round 33 (radius: 5)
[02:12:52 -93515.804017] SLOW spr round 34 (radius: 10)
[02:15:21 -93513.501646] SLOW spr round 35 (radius: 5)
[02:18:04 -93513.308596] SLOW spr round 36 (radius: 5)
[02:20:34 -93513.307107] SLOW spr round 37 (radius: 10)
[02:22:56 -93513.306952] SLOW spr round 38 (radius: 15)
[02:27:19 -93513.306934] SLOW spr round 39 (radius: 20)
[02:28:35] [worker #1] ML tree search #2, logLikelihood: -93468.666217
[02:33:28 -93513.306932] SLOW spr round 40 (radius: 25)
[02:40:44 -93513.306932] Model parameter optimization (eps = 0.100000)

[02:40:54] [worker #0] ML tree search #1, logLikelihood: -93512.968397

[02:40:54 -226804.446308] Initial branch length optimization
[02:40:57 -199346.933443] Model parameter optimization (eps = 10.000000)
[02:41:25 -199123.999369] AUTODETECT spr round 1 (radius: 5)
[02:43:43 -161583.681596] AUTODETECT spr round 2 (radius: 10)
[02:46:56 -127674.722923] AUTODETECT spr round 3 (radius: 15)
[02:50:21 -109130.528419] AUTODETECT spr round 4 (radius: 20)
[02:54:24 -104386.279636] AUTODETECT spr round 5 (radius: 25)
[02:59:10 -103438.781575] SPR radius for FAST iterations: 25 (autodetect)
[02:59:10 -103438.781575] Model parameter optimization (eps = 3.000000)
[02:59:28 -103333.105610] FAST spr round 1 (radius: 25)
[03:05:20 -94487.252503] FAST spr round 2 (radius: 25)
[03:08:56 -93853.320192] FAST spr round 3 (radius: 25)
[03:11:55 -93792.987080] FAST spr round 4 (radius: 25)
[03:14:31 -93779.096167] FAST spr round 5 (radius: 25)
[03:16:52 -93643.195512] FAST spr round 6 (radius: 25)
[03:19:05 -93643.194855] Model parameter optimization (eps = 1.000000)
[03:19:23 -93634.876505] SLOW spr round 1 (radius: 5)
[03:22:19 -93596.902254] SLOW spr round 2 (radius: 5)
[03:25:07 -93590.830691] SLOW spr round 3 (radius: 5)
[03:27:47 -93590.824134] SLOW spr round 4 (radius: 10)
[03:30:27] [worker #2] ML tree search #3, logLikelihood: -93471.895233
[03:30:31 -93585.272301] SLOW spr round 5 (radius: 5)
[03:33:37 -93584.057108] SLOW spr round 6 (radius: 5)
[03:36:33 -93581.352668] SLOW spr round 7 (radius: 5)
[03:39:21 -93578.649399] SLOW spr round 8 (radius: 5)
[03:42:04 -93577.481906] SLOW spr round 9 (radius: 5)
[03:44:40 -93577.223093] SLOW spr round 10 (radius: 5)
[03:47:17 -93577.223068] SLOW spr round 11 (radius: 10)
[03:49:53 -93577.195512] SLOW spr round 12 (radius: 15)
[03:54:30 -93577.162157] SLOW spr round 13 (radius: 20)
[04:00:49 -93577.161216] SLOW spr round 14 (radius: 25)
[04:09:05 -93575.283803] SLOW spr round 15 (radius: 5)
[04:12:23 -93543.897603] SLOW spr round 16 (radius: 5)
[04:15:18 -93543.897245] SLOW spr round 17 (radius: 10)
[04:17:58 -93543.897242] SLOW spr round 18 (radius: 15)
[04:21:59 -93543.897241] SLOW spr round 19 (radius: 20)
[04:28:19 -93543.897241] SLOW spr round 20 (radius: 25)
[04:33:39] [worker #1] ML tree search #5, logLikelihood: -93525.757336
[04:36:32 -93542.739832] SLOW spr round 21 (radius: 5)
[04:39:51 -93541.692368] SLOW spr round 22 (radius: 5)
[04:42:44 -93541.691927] SLOW spr round 23 (radius: 10)
[04:45:31 -93541.691821] SLOW spr round 24 (radius: 15)
[04:49:52 -93540.932519] SLOW spr round 25 (radius: 5)
[04:52:58 -93540.932259] SLOW spr round 26 (radius: 10)
[04:56:04 -93540.932213] SLOW spr round 27 (radius: 15)
[05:00:18 -93540.665757] SLOW spr round 28 (radius: 5)
[05:03:24 -93540.665729] SLOW spr round 29 (radius: 10)
[05:06:30 -93540.665726] SLOW spr round 30 (radius: 15)
[05:10:42 -93540.665725] SLOW spr round 31 (radius: 20)
[05:16:57 -93540.665725] SLOW spr round 32 (radius: 25)
[05:25:00 -93540.665725] Model parameter optimization (eps = 0.100000)

[05:25:07] [worker #0] ML tree search #4, logLikelihood: -93540.576245

[05:25:07 -227566.962755] Initial branch length optimization
[05:25:10 -199814.614863] Model parameter optimization (eps = 10.000000)
[05:25:39 -199537.777175] AUTODETECT spr round 1 (radius: 5)
[05:28:19 -162144.542965] AUTODETECT spr round 2 (radius: 10)
[05:31:40 -128900.706228] AUTODETECT spr round 3 (radius: 15)
[05:34:57 -112671.004702] AUTODETECT spr round 4 (radius: 20)
[05:38:33 -105560.504361] AUTODETECT spr round 5 (radius: 25)
[05:42:51 -103678.576290] SPR radius for FAST iterations: 25 (autodetect)
[05:42:51 -103678.576290] Model parameter optimization (eps = 3.000000)
[05:43:17 -103557.721867] FAST spr round 1 (radius: 25)
[05:49:04 -94814.913505] FAST spr round 2 (radius: 25)
[05:52:39 -94073.674383] FAST spr round 3 (radius: 25)
[05:55:35 -93742.247675] FAST spr round 4 (radius: 25)
[05:58:08 -93588.932058] FAST spr round 5 (radius: 25)
[06:00:27 -93583.037056] FAST spr round 6 (radius: 25)
[06:02:37 -93583.037040] Model parameter optimization (eps = 1.000000)
[06:02:54 -93581.469456] SLOW spr round 1 (radius: 5)
[06:05:49 -93561.390526] SLOW spr round 2 (radius: 5)
[06:08:38 -93558.047891] SLOW spr round 3 (radius: 5)
[06:11:19 -93556.576924] SLOW spr round 4 (radius: 5)
[06:14:00 -93550.959335] SLOW spr round 5 (radius: 5)
[06:16:36 -93550.443703] SLOW spr round 6 (radius: 5)
[06:19:11 -93550.263895] SLOW spr round 7 (radius: 5)
[06:21:44 -93550.263645] SLOW spr round 8 (radius: 10)
[06:24:25 -93544.617405] SLOW spr round 9 (radius: 5)
[06:27:33 -93540.321002] SLOW spr round 10 (radius: 5)
[06:30:23 -93539.727998] SLOW spr round 11 (radius: 5)
[06:33:02 -93539.727518] SLOW spr round 12 (radius: 10)
[06:35:45 -93538.119189] SLOW spr round 13 (radius: 5)
[06:38:50 -93535.707501] SLOW spr round 14 (radius: 5)
[06:39:26] [worker #2] ML tree search #6, logLikelihood: -93525.907235
[06:41:38 -93535.707215] SLOW spr round 15 (radius: 10)
[06:44:25 -93534.525360] SLOW spr round 16 (radius: 5)
[06:47:27 -93534.006857] SLOW spr round 17 (radius: 5)
[06:50:09 -93533.788537] SLOW spr round 18 (radius: 5)
[06:52:36 -93533.788525] SLOW spr round 19 (radius: 10)
[06:55:05 -93532.718575] SLOW spr round 20 (radius: 5)
[06:57:55 -93531.971839] SLOW spr round 21 (radius: 5)
[07:00:29 -93531.971112] SLOW spr round 22 (radius: 10)
[07:03:03 -93531.693138] SLOW spr round 23 (radius: 5)
[07:05:51 -93531.341211] SLOW spr round 24 (radius: 5)
[07:08:24 -93531.341039] SLOW spr round 25 (radius: 10)
[07:10:56 -93531.234398] SLOW spr round 26 (radius: 5)
[07:13:42 -93531.234102] SLOW spr round 27 (radius: 10)
[07:16:27 -93529.148281] SLOW spr round 28 (radius: 5)
[07:19:11 -93527.400327] SLOW spr round 29 (radius: 5)
[07:21:44 -93527.400317] SLOW spr round 30 (radius: 10)
[07:24:15 -93527.400317] SLOW spr round 31 (radius: 15)
[07:28:39 -93524.213483] SLOW spr round 32 (radius: 5)
[07:31:33 -93523.347746] SLOW spr round 33 (radius: 5)
[07:34:10 -93523.347712] SLOW spr round 34 (radius: 10)
[07:36:44 -93523.347711] SLOW spr round 35 (radius: 15)
[07:37:53] [worker #1] ML tree search #8, logLikelihood: -93517.478334
[07:41:01 -93519.272053] SLOW spr round 36 (radius: 5)
[07:43:55 -93518.798189] SLOW spr round 37 (radius: 5)
[07:46:31 -93518.798044] SLOW spr round 38 (radius: 10)
[07:49:06 -93518.730448] SLOW spr round 39 (radius: 15)
[07:53:21 -93518.730333] SLOW spr round 40 (radius: 20)
[07:59:37 -93515.762894] SLOW spr round 41 (radius: 5)
[08:02:37 -93511.128793] SLOW spr round 42 (radius: 5)
[08:05:18 -93510.118009] SLOW spr round 43 (radius: 5)
[08:07:47 -93510.116475] SLOW spr round 44 (radius: 10)
[08:10:16 -93509.168610] SLOW spr round 45 (radius: 5)
[08:13:00 -93509.166175] SLOW spr round 46 (radius: 10)
[08:15:43 -93509.166143] SLOW spr round 47 (radius: 15)
[08:19:53 -93509.166142] SLOW spr round 48 (radius: 20)
[08:26:11 -93508.990521] SLOW spr round 49 (radius: 5)
[08:29:08 -93507.722862] SLOW spr round 50 (radius: 5)
[08:31:45 -93507.721830] SLOW spr round 51 (radius: 10)
[08:34:19 -93507.721462] SLOW spr round 52 (radius: 15)
[08:38:33 -93507.721340] SLOW spr round 53 (radius: 20)
[08:44:49 -93507.721301] SLOW spr round 54 (radius: 25)
[08:52:30 -93507.721289] Model parameter optimization (eps = 0.100000)

[08:52:39] [worker #0] ML tree search #7, logLikelihood: -93507.619829

[08:52:40 -227561.708039] Initial branch length optimization
[08:52:43 -200042.011201] Model parameter optimization (eps = 10.000000)
[08:53:14 -199748.070712] AUTODETECT spr round 1 (radius: 5)
[08:55:40 -162925.148012] AUTODETECT spr round 2 (radius: 10)
[08:58:44 -128925.192127] AUTODETECT spr round 3 (radius: 15)
[09:01:56 -108365.133828] AUTODETECT spr round 4 (radius: 20)
[09:05:25 -104215.153751] AUTODETECT spr round 5 (radius: 25)
[09:09:42 -103183.083083] SPR radius for FAST iterations: 25 (autodetect)
[09:09:42 -103183.083083] Model parameter optimization (eps = 3.000000)
[09:10:10 -103092.198668] FAST spr round 1 (radius: 25)
[09:15:06 -94397.660974] FAST spr round 2 (radius: 25)
[09:18:24 -93654.033314] FAST spr round 3 (radius: 25)
[09:21:00 -93598.232622] FAST spr round 4 (radius: 25)
[09:23:19 -93589.167813] FAST spr round 5 (radius: 25)
[09:25:25 -93588.349691] FAST spr round 6 (radius: 25)
[09:27:25 -93588.348434] Model parameter optimization (eps = 1.000000)
[09:27:41 -93583.664163] SLOW spr round 1 (radius: 5)
[09:30:29 -93561.084600] SLOW spr round 2 (radius: 5)
[09:33:11 -93555.425181] SLOW spr round 3 (radius: 5)
[09:35:48 -93550.954675] SLOW spr round 4 (radius: 5)
[09:38:22 -93550.004765] SLOW spr round 5 (radius: 5)
[09:40:56 -93549.250384] SLOW spr round 6 (radius: 5)
[09:43:29 -93546.335370] SLOW spr round 7 (radius: 5)
[09:44:43] [worker #1] ML tree search #11, logLikelihood: -93478.998449
[09:46:01 -93546.015793] SLOW spr round 8 (radius: 5)
[09:48:32 -93546.015734] SLOW spr round 9 (radius: 10)
[09:48:41] [worker #2] ML tree search #9, logLikelihood: -93491.466531
[09:51:14 -93533.754369] SLOW spr round 10 (radius: 5)
[09:54:20 -93527.540260] SLOW spr round 11 (radius: 5)
[09:57:06 -93523.515835] SLOW spr round 12 (radius: 5)
[09:59:44 -93523.308872] SLOW spr round 13 (radius: 5)
[10:02:16 -93523.308850] SLOW spr round 14 (radius: 10)
[10:04:54 -93523.308836] SLOW spr round 15 (radius: 15)
[10:09:47 -93515.416587] SLOW spr round 16 (radius: 5)
[10:12:55 -93507.823232] SLOW spr round 17 (radius: 5)
[10:15:43 -93507.175128] SLOW spr round 18 (radius: 5)
[10:18:22 -93507.174824] SLOW spr round 19 (radius: 10)
[10:21:03 -93505.243253] SLOW spr round 20 (radius: 5)
[10:24:04 -93500.554151] SLOW spr round 21 (radius: 5)
[10:26:47 -93500.553901] SLOW spr round 22 (radius: 10)
[10:29:31 -93500.553898] SLOW spr round 23 (radius: 15)
[10:34:10 -93500.553898] SLOW spr round 24 (radius: 20)
[10:40:40 -93499.816024] SLOW spr round 25 (radius: 5)
[10:43:55 -93494.643975] SLOW spr round 26 (radius: 5)
[10:46:43 -93494.387250] SLOW spr round 27 (radius: 5)
[10:49:21 -93494.386885] SLOW spr round 28 (radius: 10)
[10:52:01 -93494.386878] SLOW spr round 29 (radius: 15)
[10:56:15 -93494.386878] SLOW spr round 30 (radius: 20)
[11:01:43 -93494.386877] SLOW spr round 31 (radius: 25)
[11:09:09 -93494.038624] SLOW spr round 32 (radius: 5)
[11:12:23 -93493.990404] SLOW spr round 33 (radius: 10)
[11:15:45 -93493.988109] SLOW spr round 34 (radius: 15)
[11:20:11 -93493.987311] SLOW spr round 35 (radius: 20)
[11:26:48 -93492.295479] SLOW spr round 36 (radius: 5)
[11:29:58 -93492.295476] SLOW spr round 37 (radius: 10)
[11:33:14 -93492.295476] SLOW spr round 38 (radius: 15)
[11:37:43 -93492.295475] SLOW spr round 39 (radius: 20)
[11:44:16 -93492.295475] SLOW spr round 40 (radius: 25)
[11:52:26 -93492.295474] Model parameter optimization (eps = 0.100000)

[11:52:38] [worker #0] ML tree search #10, logLikelihood: -93492.021727

[11:52:38 -227491.852757] Initial branch length optimization
[11:52:41 -199505.129381] Model parameter optimization (eps = 10.000000)
[11:53:09 -199227.415148] AUTODETECT spr round 1 (radius: 5)
[11:55:51 -164181.748028] AUTODETECT spr round 2 (radius: 10)
[11:58:55 -127517.012956] AUTODETECT spr round 3 (radius: 15)
[12:02:14 -113564.339002] AUTODETECT spr round 4 (radius: 20)
[12:06:12 -107194.630146] AUTODETECT spr round 5 (radius: 25)
[12:10:22 -104195.683993] SPR radius for FAST iterations: 25 (autodetect)
[12:10:22 -104195.683993] Model parameter optimization (eps = 3.000000)
[12:10:47 -104087.121125] FAST spr round 1 (radius: 25)
[12:13:39] [worker #1] ML tree search #14, logLikelihood: -93537.113746
[12:16:33 -94374.453142] FAST spr round 2 (radius: 25)
[12:20:08 -93697.517286] FAST spr round 3 (radius: 25)
[12:23:05 -93630.935675] FAST spr round 4 (radius: 25)
[12:25:42 -93613.664030] FAST spr round 5 (radius: 25)
[12:28:00 -93613.428109] FAST spr round 6 (radius: 25)
[12:30:15 -93613.121092] FAST spr round 7 (radius: 25)
[12:32:26 -93613.121053] Model parameter optimization (eps = 1.000000)
[12:32:46 -93600.037325] SLOW spr round 1 (radius: 5)
[12:35:43 -93557.505698] SLOW spr round 2 (radius: 5)
[12:38:30 -93552.526642] SLOW spr round 3 (radius: 5)
[12:41:09 -93552.026499] SLOW spr round 4 (radius: 5)
[12:43:46 -93552.026291] SLOW spr round 5 (radius: 10)
[12:43:51] [worker #2] ML tree search #12, logLikelihood: -93533.338565
[12:46:35 -93545.513480] SLOW spr round 6 (radius: 5)
[12:49:43 -93544.668699] SLOW spr round 7 (radius: 5)
[12:52:32 -93544.668688] SLOW spr round 8 (radius: 10)
[12:55:23 -93544.047328] SLOW spr round 9 (radius: 5)
[12:58:26 -93543.988225] SLOW spr round 10 (radius: 10)
[13:01:32 -93543.958377] SLOW spr round 11 (radius: 15)
[13:06:22 -93541.637254] SLOW spr round 12 (radius: 5)
[13:09:33 -93541.637191] SLOW spr round 13 (radius: 10)
[13:12:48 -93540.829983] SLOW spr round 14 (radius: 5)
[13:15:55 -93539.920451] SLOW spr round 15 (radius: 5)
[13:18:45 -93539.920391] SLOW spr round 16 (radius: 10)
[13:21:36 -93539.920391] SLOW spr round 17 (radius: 15)
[13:26:33 -93539.236808] SLOW spr round 18 (radius: 5)
[13:29:46 -93539.236808] SLOW spr round 19 (radius: 10)
[13:33:03 -93539.236808] SLOW spr round 20 (radius: 15)
[13:37:47 -93539.026750] SLOW spr round 21 (radius: 5)
[13:40:59 -93539.026570] SLOW spr round 22 (radius: 10)
[13:44:16 -93539.026568] SLOW spr round 23 (radius: 15)
[13:49:02 -93536.373971] SLOW spr round 24 (radius: 5)
[13:52:19 -93533.922057] SLOW spr round 25 (radius: 5)
[13:55:16 -93532.872705] SLOW spr round 26 (radius: 5)
[13:58:01 -93532.282953] SLOW spr round 27 (radius: 5)
[14:00:40 -93532.282555] SLOW spr round 28 (radius: 10)
[14:03:27 -93531.576299] SLOW spr round 29 (radius: 5)
[14:06:37 -93531.152558] SLOW spr round 30 (radius: 5)
[14:09:29 -93531.152254] SLOW spr round 31 (radius: 10)
[14:12:19 -93531.152245] SLOW spr round 32 (radius: 15)
[14:17:16 -93530.848770] SLOW spr round 33 (radius: 5)
[14:20:26 -93530.221103] SLOW spr round 34 (radius: 5)
[14:23:18 -93530.220472] SLOW spr round 35 (radius: 10)
[14:26:10 -93530.220467] SLOW spr round 36 (radius: 15)
[14:31:08 -93529.835673] SLOW spr round 37 (radius: 5)
[14:34:26 -93527.904161] SLOW spr round 38 (radius: 5)
[14:37:19 -93527.903949] SLOW spr round 39 (radius: 10)
[14:40:12 -93527.903948] SLOW spr round 40 (radius: 15)
[14:45:06 -93527.903948] SLOW spr round 41 (radius: 20)
[14:52:28 -93523.889133] SLOW spr round 42 (radius: 5)
[14:55:43 -93523.887686] SLOW spr round 43 (radius: 10)
[14:59:05 -93523.887587] SLOW spr round 44 (radius: 15)
[15:03:54 -93523.887578] SLOW spr round 45 (radius: 20)
[15:09:29] [worker #1] ML tree search #17, logLikelihood: -93554.128800
[15:11:20 -93523.812293] SLOW spr round 46 (radius: 25)
[15:20:15] [worker #2] ML tree search #15, logLikelihood: -93488.219981
[15:20:39 -93521.946856] SLOW spr round 47 (radius: 5)
[15:23:57 -93521.585007] SLOW spr round 48 (radius: 5)
[15:26:55 -93521.126800] SLOW spr round 49 (radius: 5)
[15:29:42 -93521.126162] SLOW spr round 50 (radius: 10)
[15:32:34 -93518.666419] SLOW spr round 51 (radius: 5)
[15:35:40 -93511.194810] SLOW spr round 52 (radius: 5)
[15:38:29 -93511.194683] SLOW spr round 53 (radius: 10)
[15:41:18 -93511.141946] SLOW spr round 54 (radius: 15)
[15:46:15 -93511.052464] SLOW spr round 55 (radius: 20)
[15:53:12 -93510.383712] SLOW spr round 56 (radius: 5)
[15:56:29 -93508.311080] SLOW spr round 57 (radius: 5)
[15:59:27 -93506.676446] SLOW spr round 58 (radius: 5)
[16:02:11 -93506.254548] SLOW spr round 59 (radius: 5)
[16:04:53 -93506.254109] SLOW spr round 60 (radius: 10)
[16:07:40 -93506.254068] SLOW spr round 61 (radius: 15)
[16:12:38 -93506.254064] SLOW spr round 62 (radius: 20)
[16:19:24 -93506.254063] SLOW spr round 63 (radius: 25)
[16:27:51 -93506.254063] Model parameter optimization (eps = 0.100000)

[16:27:59] [worker #0] ML tree search #13, logLikelihood: -93506.204465

[16:27:59 -226822.945384] Initial branch length optimization
[16:28:02 -199293.621628] Model parameter optimization (eps = 10.000000)
[16:28:35 -199055.458956] AUTODETECT spr round 1 (radius: 5)
[16:31:15 -161036.757353] AUTODETECT spr round 2 (radius: 10)
[16:34:32 -127951.344391] AUTODETECT spr round 3 (radius: 15)
[16:37:56 -112535.132734] AUTODETECT spr round 4 (radius: 20)
[16:41:48 -105793.496096] AUTODETECT spr round 5 (radius: 25)
[16:46:31 -104113.748623] SPR radius for FAST iterations: 25 (autodetect)
[16:46:31 -104113.748623] Model parameter optimization (eps = 3.000000)
[16:46:49 -104007.946256] FAST spr round 1 (radius: 25)
[16:51:14 -94475.249471] FAST spr round 2 (radius: 25)
[16:53:23] [worker #1] ML tree search #20, logLikelihood: -93530.668430
[16:54:13 -93808.728705] FAST spr round 3 (radius: 25)
[16:56:45 -93641.148648] FAST spr round 4 (radius: 25)
[16:59:23 -93610.036950] FAST spr round 5 (radius: 25)
[17:01:45 -93593.958978] FAST spr round 6 (radius: 25)
[17:03:58 -93584.451428] FAST spr round 7 (radius: 25)
[17:06:04 -93583.019471] FAST spr round 8 (radius: 25)
[17:08:07 -93583.018476] Model parameter optimization (eps = 1.000000)
[17:08:21 -93578.424353] SLOW spr round 1 (radius: 5)
[17:11:10 -93560.692581] SLOW spr round 2 (radius: 5)
[17:13:52 -93556.529443] SLOW spr round 3 (radius: 5)
[17:16:32 -93552.464457] SLOW spr round 4 (radius: 5)
[17:19:06 -93551.450868] SLOW spr round 5 (radius: 5)
[17:21:38 -93551.450858] SLOW spr round 6 (radius: 10)
[17:24:15 -93546.933594] SLOW spr round 7 (radius: 5)
[17:27:22 -93539.293730] SLOW spr round 8 (radius: 5)
[17:30:15 -93534.567399] SLOW spr round 9 (radius: 5)
[17:32:53 -93534.566642] SLOW spr round 10 (radius: 10)
[17:33:09] [worker #2] ML tree search #18, logLikelihood: -93547.947205
[17:35:31 -93534.566605] SLOW spr round 11 (radius: 15)
[17:40:15 -93524.853097] SLOW spr round 12 (radius: 5)
[17:43:26 -93522.549755] SLOW spr round 13 (radius: 5)
[17:46:14 -93522.549025] SLOW spr round 14 (radius: 10)
[17:48:57 -93522.548758] SLOW spr round 15 (radius: 15)
[17:53:31 -93520.746172] SLOW spr round 16 (radius: 5)
[17:56:42 -93520.045182] SLOW spr round 17 (radius: 5)
[17:59:31 -93520.044818] SLOW spr round 18 (radius: 10)
[18:02:14 -93520.044769] SLOW spr round 19 (radius: 15)
[18:06:47 -93519.694902] SLOW spr round 20 (radius: 5)
[18:09:55 -93519.491367] SLOW spr round 21 (radius: 5)
[18:12:44 -93519.491290] SLOW spr round 22 (radius: 10)
[18:15:27 -93519.491234] SLOW spr round 23 (radius: 15)
[18:19:59 -93519.442373] SLOW spr round 24 (radius: 20)
[18:26:40 -93519.442277] SLOW spr round 25 (radius: 25)
[18:35:20 -93519.406701] Model parameter optimization (eps = 0.100000)

[18:35:33] [worker #0] ML tree search #16, logLikelihood: -93519.299911

[18:35:33 -225746.231024] Initial branch length optimization
[18:35:36 -198456.897583] Model parameter optimization (eps = 10.000000)
[18:36:08 -198226.104894] AUTODETECT spr round 1 (radius: 5)
[18:38:48 -161960.287157] AUTODETECT spr round 2 (radius: 10)
[18:41:55 -124795.826955] AUTODETECT spr round 3 (radius: 15)
[18:45:05 -112256.696721] AUTODETECT spr round 4 (radius: 20)
[18:48:43 -105312.565450] AUTODETECT spr round 5 (radius: 25)
[18:53:45 -103433.652171] SPR radius for FAST iterations: 25 (autodetect)
[18:53:45 -103433.652171] Model parameter optimization (eps = 3.000000)
[18:54:17 -103326.043481] FAST spr round 1 (radius: 25)
[18:59:57 -94204.530288] FAST spr round 2 (radius: 25)
[19:03:18 -93684.187258] FAST spr round 3 (radius: 25)
[19:06:08 -93621.635954] FAST spr round 4 (radius: 25)
[19:08:37 -93602.878664] FAST spr round 5 (radius: 25)
[19:10:49 -93600.366522] FAST spr round 6 (radius: 25)
[19:12:56 -93598.306570] FAST spr round 7 (radius: 25)
[19:14:59 -93598.306377] Model parameter optimization (eps = 1.000000)
[19:15:13 -93595.307871] SLOW spr round 1 (radius: 5)
[19:17:57 -93560.822429] SLOW spr round 2 (radius: 5)
[19:20:33 -93558.607556] SLOW spr round 3 (radius: 5)
[19:23:03 -93558.607506] SLOW spr round 4 (radius: 10)
[19:25:45 -93551.175636] SLOW spr round 5 (radius: 5)
[19:28:47 -93547.582456] SLOW spr round 6 (radius: 5)
[19:31:34 -93541.348883] SLOW spr round 7 (radius: 5)
[19:34:15 -93538.815334] SLOW spr round 8 (radius: 5)
[19:36:49 -93538.814175] SLOW spr round 9 (radius: 10)
[19:39:27 -93536.865953] SLOW spr round 10 (radius: 5)
[19:42:28 -93535.909965] SLOW spr round 11 (radius: 5)
[19:45:10 -93535.696165] SLOW spr round 12 (radius: 5)
[19:47:45 -93535.695964] SLOW spr round 13 (radius: 10)
[19:50:21 -93535.438908] SLOW spr round 14 (radius: 5)
[19:53:17 -93535.438379] SLOW spr round 15 (radius: 10)
[19:56:15 -93535.349613] SLOW spr round 16 (radius: 15)
[20:00:48 -93532.962697] SLOW spr round 17 (radius: 5)
[20:03:51 -93532.962681] SLOW spr round 18 (radius: 10)
[20:07:00 -93532.342455] SLOW spr round 19 (radius: 5)
[20:09:52 -93530.748198] SLOW spr round 20 (radius: 5)
[20:12:32 -93529.721610] SLOW spr round 21 (radius: 5)
[20:15:02 -93529.721504] SLOW spr round 22 (radius: 10)
[20:17:35 -93529.721503] SLOW spr round 23 (radius: 15)
[20:22:21 -93529.615638] SLOW spr round 24 (radius: 5)
[20:25:21 -93526.900952] SLOW spr round 25 (radius: 5)
[20:28:03 -93525.660026] SLOW spr round 26 (radius: 5)
[20:30:36 -93525.659927] SLOW spr round 27 (radius: 10)
[20:33:00 -93525.353126] SLOW spr round 28 (radius: 5)
[20:35:27 -93525.353003] SLOW spr round 29 (radius: 10)
[20:37:54 -93525.353002] SLOW spr round 30 (radius: 15)
[20:41:36 -93525.353002] SLOW spr round 31 (radius: 20)
[20:47:28 -93525.353002] SLOW spr round 32 (radius: 25)
[20:54:50 -93525.353002] Model parameter optimization (eps = 0.100000)

[20:54:56] [worker #0] ML tree search #19, logLikelihood: -93525.295623


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.174031,0.304016) (0.219496,0.408709) (0.447956,1.171678) (0.158517,2.097697) 
   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: -93468.666217

AIC score: 190943.332433 / AICc score: 8218967.332433 / BIC score: 197152.364888
Free parameters (model + branch lengths): 2003

WARNING: Number of free parameters (K=2003) is larger than alignment size (n=164).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 34 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A1L4H1/3_mltree/A1L4H1.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A1L4H1/3_mltree/A1L4H1.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A1L4H1/3_mltree/A1L4H1.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A1L4H1/3_mltree/A1L4H1.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A1L4H1/3_mltree/A1L4H1.raxml.log

Analysis started: 05-Jul-2021 17:40:31 / finished: 06-Jul-2021 14:35:28

Elapsed time: 75297.013 seconds

Consumed energy: 6578.415 Wh (= 33 km in an electric car, or 164 km with an e-scooter!)