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 01-Jul-2021 10:25:32 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JC4/2_msa/Q96JC4_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JC4/3_mltree/Q96JC4 --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/Q96JC4/2_msa/Q96JC4_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 587 sites

WARNING: Sequences tr_A0A2I2YQQ8_A0A2I2YQQ8_GORGO_9595 and sp_Q9Y2G7_ZFP30_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2I2YYI0_A0A2I2YYI0_GORGO_9595 and tr_A0A2K5NSA5_A0A2K5NSA5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I2YYI0_A0A2I2YYI0_GORGO_9595 and tr_A0A2K5YEE6_A0A2K5YEE6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G3RFV8_G3RFV8_GORGO_9595 and tr_A0A2J8JLI6_A0A2J8JLI6_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RFV8_G3RFV8_GORGO_9595 and sp_Q96ND8_ZN583_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A2J8QIH1_A0A2J8QIH1_PANTR_9598 and tr_A0A2R9AKC8_A0A2R9AKC8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A1D5R403_A0A1D5R403_MACMU_9544 and tr_A0A2K6CQR3_A0A2K6CQR3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6QVW9_F6QVW9_MACMU_9544 and tr_A0A0A0MUP5_A0A0A0MUP5_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6QVW9_F6QVW9_MACMU_9544 and tr_A0A2K5MYE8_A0A2K5MYE8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F6QVW9_F6QVW9_MACMU_9544 and tr_A0A2K5ZQH5_A0A2K5ZQH5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F6UR85_F6UR85_MACMU_9544 and tr_A0A2K6ADH3_A0A2K6ADH3_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7C0K1_F7C0K1_MACMU_9544 and tr_A0A2K6B5R4_A0A2K6B5R4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7F0N9_F7F0N9_MACMU_9544 and tr_A0A2K5LZF8_A0A2K5LZF8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7F0N9_F7F0N9_MACMU_9544 and tr_A0A2K6B2T5_A0A2K6B2T5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7F0N9_F7F0N9_MACMU_9544 and tr_A0A2K5YGT5_A0A2K5YGT5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F7GB84_F7GB84_MACMU_9544 and tr_A0A2K6BN44_A0A2K6BN44_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7GTJ8_F7GTJ8_MACMU_9544 and tr_A0A2K6BJH0_A0A2K6BJH0_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7H5I5_F7H5I5_MACMU_9544 and tr_G7PXE5_G7PXE5_MACFA_9541 are exactly identical!
WARNING: Sequences tr_A0A2U3V7M1_A0A2U3V7M1_TURTR_9739 and tr_A0A2U4ATW9_A0A2U4ATW9_TURTR_9739 are exactly identical!
WARNING: Sequences tr_A0A2U3XJ70_A0A2U3XJ70_LEPWE_9713 and tr_A0A2Y9L647_A0A2Y9L647_ENHLU_391180 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/Q96JC4/3_mltree/Q96JC4.raxml.reduced.phy

Alignment comprises 1 partitions and 587 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 587 / 587
Gaps: 14.23 %
Invariant sites: 0.17 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JC4/3_mltree/Q96JC4.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 / 84 / 6720
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -734508.676563] Initial branch length optimization
[00:00:03 -648818.981645] Model parameter optimization (eps = 10.000000)
[00:00:54 -647062.559532] AUTODETECT spr round 1 (radius: 5)
[00:04:35 -516358.277165] AUTODETECT spr round 2 (radius: 10)
[00:07:24 -341192.767902] AUTODETECT spr round 3 (radius: 15)
[00:09:36 -268404.700362] AUTODETECT spr round 4 (radius: 20)
[00:12:28 -238702.352569] AUTODETECT spr round 5 (radius: 25)
[00:15:27 -236977.067047] SPR radius for FAST iterations: 25 (autodetect)
[00:15:27 -236977.067047] Model parameter optimization (eps = 3.000000)
[00:15:51 -236647.643656] FAST spr round 1 (radius: 25)
[00:17:56 -204674.937442] FAST spr round 2 (radius: 25)
[00:19:44 -203331.064671] FAST spr round 3 (radius: 25)
[00:21:23 -203189.629437] FAST spr round 4 (radius: 25)
[00:22:55 -203182.001672] FAST spr round 5 (radius: 25)
[00:25:36 -203165.721465] FAST spr round 6 (radius: 25)
[00:27:57 -203165.721274] Model parameter optimization (eps = 1.000000)
[00:28:08 -203161.288838] SLOW spr round 1 (radius: 5)
[00:30:10 -203066.551582] SLOW spr round 2 (radius: 5)
[00:32:01 -203054.708989] SLOW spr round 3 (radius: 5)
[00:33:33 -203054.708838] SLOW spr round 4 (radius: 10)
[00:35:11 -203054.244758] SLOW spr round 5 (radius: 5)
[00:37:02 -203054.244399] SLOW spr round 6 (radius: 10)
[00:38:52 -203054.180706] SLOW spr round 7 (radius: 15)
[00:42:08 -203054.180250] SLOW spr round 8 (radius: 20)
[00:47:36 -203044.213795] SLOW spr round 9 (radius: 5)
[00:49:53 -203042.264178] SLOW spr round 10 (radius: 5)
[00:51:51 -203042.263864] SLOW spr round 11 (radius: 10)
[00:53:47 -203037.575442] SLOW spr round 12 (radius: 5)
[00:55:52 -203035.578488] SLOW spr round 13 (radius: 5)
[00:57:43 -203035.578129] SLOW spr round 14 (radius: 10)
[00:59:36 -203035.577820] SLOW spr round 15 (radius: 15)
[01:03:20 -203035.577510] SLOW spr round 16 (radius: 20)
[01:08:41 -203035.577249] SLOW spr round 17 (radius: 25)
[01:13:40 -203035.577245] Model parameter optimization (eps = 0.100000)

[01:13:46] ML tree search #1, logLikelihood: -203035.373364

[01:13:46 -737916.569145] Initial branch length optimization
[01:13:49 -649187.046265] Model parameter optimization (eps = 10.000000)
[01:14:16 -647422.512634] AUTODETECT spr round 1 (radius: 5)
[01:16:10 -535686.651162] AUTODETECT spr round 2 (radius: 10)
[01:18:29 -365789.170529] AUTODETECT spr round 3 (radius: 15)
[01:20:43 -256860.903251] AUTODETECT spr round 4 (radius: 20)
[01:23:26 -238370.810919] AUTODETECT spr round 5 (radius: 25)
[01:26:36 -237019.795447] SPR radius for FAST iterations: 25 (autodetect)
[01:26:36 -237019.795447] Model parameter optimization (eps = 3.000000)
[01:26:51 -236637.838021] FAST spr round 1 (radius: 25)
[01:28:47 -205042.236520] FAST spr round 2 (radius: 25)
[01:30:30 -203328.640691] FAST spr round 3 (radius: 25)
[01:32:06 -203185.519720] FAST spr round 4 (radius: 25)
[01:33:36 -203164.988669] FAST spr round 5 (radius: 25)
[01:35:01 -203144.608764] FAST spr round 6 (radius: 25)
[01:36:25 -203144.608742] Model parameter optimization (eps = 1.000000)
[01:36:38 -203135.049308] SLOW spr round 1 (radius: 5)
[01:38:33 -203070.042261] SLOW spr round 2 (radius: 5)
[01:40:23 -203064.880148] SLOW spr round 3 (radius: 5)
[01:42:08 -203064.880125] SLOW spr round 4 (radius: 10)
[01:44:00 -203064.880125] SLOW spr round 5 (radius: 15)
[01:47:50 -203064.880125] SLOW spr round 6 (radius: 20)
[01:53:04 -203064.880125] SLOW spr round 7 (radius: 25)
[01:58:10 -203064.880125] Model parameter optimization (eps = 0.100000)

[01:58:18] ML tree search #2, logLikelihood: -203064.599457

[01:58:18 -735841.203036] Initial branch length optimization
[01:58:20 -650285.586015] Model parameter optimization (eps = 10.000000)
[01:58:55 -648461.280958] AUTODETECT spr round 1 (radius: 5)
[02:00:51 -522179.986253] AUTODETECT spr round 2 (radius: 10)
[02:02:57 -341669.737422] AUTODETECT spr round 3 (radius: 15)
[02:05:14 -258476.203188] AUTODETECT spr round 4 (radius: 20)
[02:07:54 -238572.050998] AUTODETECT spr round 5 (radius: 25)
[02:11:10 -238051.410936] SPR radius for FAST iterations: 25 (autodetect)
[02:11:10 -238051.410936] Model parameter optimization (eps = 3.000000)
[02:11:26 -237769.327821] FAST spr round 1 (radius: 25)
[02:13:28 -203932.562239] FAST spr round 2 (radius: 25)
[02:15:09 -203297.754215] FAST spr round 3 (radius: 25)
[02:16:44 -203164.325848] FAST spr round 4 (radius: 25)
[02:18:12 -203159.693356] FAST spr round 5 (radius: 25)
[02:19:38 -203158.887335] FAST spr round 6 (radius: 25)
[02:21:01 -203158.887330] Model parameter optimization (eps = 1.000000)
[02:21:14 -203154.971363] SLOW spr round 1 (radius: 5)
[02:23:06 -203093.660353] SLOW spr round 2 (radius: 5)
[02:24:54 -203073.736488] SLOW spr round 3 (radius: 5)
[02:26:43 -203072.074228] SLOW spr round 4 (radius: 5)
[02:28:27 -203071.049514] SLOW spr round 5 (radius: 5)
[02:30:11 -203071.048973] SLOW spr round 6 (radius: 10)
[02:32:02 -203071.048454] SLOW spr round 7 (radius: 15)
[02:35:53 -203071.047935] SLOW spr round 8 (radius: 20)
[02:40:52 -203071.047416] SLOW spr round 9 (radius: 25)
[02:45:37 -203071.046897] Model parameter optimization (eps = 0.100000)

[02:45:42] ML tree search #3, logLikelihood: -203070.914920

[02:45:42 -739688.933977] Initial branch length optimization
[02:45:44 -651562.522780] Model parameter optimization (eps = 10.000000)
[02:46:08 -649657.710493] AUTODETECT spr round 1 (radius: 5)
[02:48:06 -528274.818688] AUTODETECT spr round 2 (radius: 10)
[02:50:16 -337483.078802] AUTODETECT spr round 3 (radius: 15)
[02:52:27 -257499.953932] AUTODETECT spr round 4 (radius: 20)
[02:55:12 -241271.791132] AUTODETECT spr round 5 (radius: 25)
[02:58:10 -239567.570340] SPR radius for FAST iterations: 25 (autodetect)
[02:58:10 -239567.570340] Model parameter optimization (eps = 3.000000)
[02:58:27 -239278.659788] FAST spr round 1 (radius: 25)
[03:00:28 -204952.651679] FAST spr round 2 (radius: 25)
[03:02:11 -203293.356054] FAST spr round 3 (radius: 25)
[03:03:47 -203180.735279] FAST spr round 4 (radius: 25)
[03:05:14 -203152.564974] FAST spr round 5 (radius: 25)
[03:06:38 -203152.564420] Model parameter optimization (eps = 1.000000)
[03:06:50 -203149.549646] SLOW spr round 1 (radius: 5)
[03:08:42 -203082.258745] SLOW spr round 2 (radius: 5)
[03:10:21 -203076.095010] SLOW spr round 3 (radius: 5)
[03:12:05 -203068.430765] SLOW spr round 4 (radius: 5)
[03:13:52 -203062.294217] SLOW spr round 5 (radius: 5)
[03:15:37 -203055.753101] SLOW spr round 6 (radius: 5)
[03:17:21 -203055.753076] SLOW spr round 7 (radius: 10)
[03:19:13 -203055.375889] SLOW spr round 8 (radius: 5)
[03:21:23 -203055.234347] SLOW spr round 9 (radius: 5)
[03:23:15 -203055.234323] SLOW spr round 10 (radius: 10)
[03:25:09 -203055.072251] SLOW spr round 11 (radius: 5)
[03:27:19 -203055.072247] SLOW spr round 12 (radius: 10)
[03:29:25 -203055.072247] SLOW spr round 13 (radius: 15)
[03:33:05 -203055.072247] SLOW spr round 14 (radius: 20)
[03:38:40 -203055.072247] SLOW spr round 15 (radius: 25)
[03:43:39 -203055.072247] Model parameter optimization (eps = 0.100000)

[03:43:46] ML tree search #4, logLikelihood: -203054.946366

[03:43:46 -735944.456249] Initial branch length optimization
[03:43:48 -651642.560764] Model parameter optimization (eps = 10.000000)
[03:44:15 -649636.890842] AUTODETECT spr round 1 (radius: 5)
[03:46:14 -521492.406040] AUTODETECT spr round 2 (radius: 10)
[03:48:24 -337341.194042] AUTODETECT spr round 3 (radius: 15)
[03:50:37 -252874.212462] AUTODETECT spr round 4 (radius: 20)
[03:53:23 -234670.788199] AUTODETECT spr round 5 (radius: 25)
[03:56:21 -233223.757579] SPR radius for FAST iterations: 25 (autodetect)
[03:56:21 -233223.757579] Model parameter optimization (eps = 3.000000)
[03:56:43 -232946.080516] FAST spr round 1 (radius: 25)
[03:58:42 -204470.519190] FAST spr round 2 (radius: 25)
[04:00:22 -203342.199110] FAST spr round 3 (radius: 25)
[04:01:57 -203146.583007] FAST spr round 4 (radius: 25)
[04:03:24 -203133.231021] FAST spr round 5 (radius: 25)
[04:04:48 -203123.671634] FAST spr round 6 (radius: 25)
[04:06:11 -203123.671633] Model parameter optimization (eps = 1.000000)
[04:06:24 -203116.137738] SLOW spr round 1 (radius: 5)
[04:08:09 -203079.411103] SLOW spr round 2 (radius: 5)
[04:09:55 -203066.542858] SLOW spr round 3 (radius: 5)
[04:11:36 -203066.053527] SLOW spr round 4 (radius: 5)
[04:13:17 -203066.053471] SLOW spr round 5 (radius: 10)
[04:15:03 -203066.028937] SLOW spr round 6 (radius: 15)
[04:18:39 -203066.028890] SLOW spr round 7 (radius: 20)
[04:23:43 -203066.028890] SLOW spr round 8 (radius: 25)
[04:28:50 -203066.028889] Model parameter optimization (eps = 0.100000)

[04:28:58] ML tree search #5, logLikelihood: -203065.582576

[04:28:58 -735406.544894] Initial branch length optimization
[04:29:00 -649011.423028] Model parameter optimization (eps = 10.000000)
[04:29:28 -647261.956252] AUTODETECT spr round 1 (radius: 5)
[04:31:21 -525580.719235] AUTODETECT spr round 2 (radius: 10)
[04:33:35 -347174.225958] AUTODETECT spr round 3 (radius: 15)
[04:35:56 -252103.434076] AUTODETECT spr round 4 (radius: 20)
[04:38:54 -237528.667827] AUTODETECT spr round 5 (radius: 25)
[04:41:47 -233279.728489] SPR radius for FAST iterations: 25 (autodetect)
[04:41:47 -233279.728489] Model parameter optimization (eps = 3.000000)
[04:42:03 -233016.186279] FAST spr round 1 (radius: 25)
[04:43:58 -204352.042048] FAST spr round 2 (radius: 25)
[04:45:36 -203190.793336] FAST spr round 3 (radius: 25)
[04:47:32 -203154.609704] FAST spr round 4 (radius: 25)
[04:50:09 -203147.635657] FAST spr round 5 (radius: 25)
[04:51:32 -203147.635607] Model parameter optimization (eps = 1.000000)
[04:51:43 -203138.205762] SLOW spr round 1 (radius: 5)
[04:53:38 -203081.773856] SLOW spr round 2 (radius: 5)
[04:55:28 -203074.418533] SLOW spr round 3 (radius: 5)
[04:57:19 -203074.418270] SLOW spr round 4 (radius: 10)
[04:59:15 -203070.129530] SLOW spr round 5 (radius: 5)
[05:01:30 -203060.181568] SLOW spr round 6 (radius: 5)
[05:03:22 -203059.678088] SLOW spr round 7 (radius: 5)
[05:05:03 -203059.678085] SLOW spr round 8 (radius: 10)
[05:06:44 -203059.678085] SLOW spr round 9 (radius: 15)
[05:10:12 -203059.678085] SLOW spr round 10 (radius: 20)
[05:16:30 -203059.678085] SLOW spr round 11 (radius: 25)
[05:21:19 -203059.678085] Model parameter optimization (eps = 0.100000)

[05:21:25] ML tree search #6, logLikelihood: -203059.521535

[05:21:25 -733524.696332] Initial branch length optimization
[05:21:27 -649437.375253] Model parameter optimization (eps = 10.000000)
[05:21:53 -647553.706948] AUTODETECT spr round 1 (radius: 5)
[05:23:33 -517431.424329] AUTODETECT spr round 2 (radius: 10)
[05:25:30 -343775.242371] AUTODETECT spr round 3 (radius: 15)
[05:27:35 -263754.776410] AUTODETECT spr round 4 (radius: 20)
[05:30:19 -242364.187973] AUTODETECT spr round 5 (radius: 25)
[05:33:21 -239916.538049] SPR radius for FAST iterations: 25 (autodetect)
[05:33:21 -239916.538049] Model parameter optimization (eps = 3.000000)
[05:33:42 -239601.868083] FAST spr round 1 (radius: 25)
[05:35:47 -204670.963406] FAST spr round 2 (radius: 25)
[05:37:35 -203327.799203] FAST spr round 3 (radius: 25)
[05:39:14 -203193.973156] FAST spr round 4 (radius: 25)
[05:40:46 -203127.102202] FAST spr round 5 (radius: 25)
[05:42:15 -203118.217673] FAST spr round 6 (radius: 25)
[05:43:44 -203118.217604] Model parameter optimization (eps = 1.000000)
[05:43:53 -203113.042017] SLOW spr round 1 (radius: 5)
[05:45:52 -203055.946897] SLOW spr round 2 (radius: 5)
[05:47:46 -203046.365476] SLOW spr round 3 (radius: 5)
[05:49:37 -203046.365163] SLOW spr round 4 (radius: 10)
[05:51:35 -203044.456928] SLOW spr round 5 (radius: 5)
[05:53:46 -203041.695206] SLOW spr round 6 (radius: 5)
[05:55:43 -203041.695144] SLOW spr round 7 (radius: 10)
[05:57:41 -203041.695135] SLOW spr round 8 (radius: 15)
[06:01:35 -203041.695133] SLOW spr round 9 (radius: 20)
[06:07:15 -203041.695132] SLOW spr round 10 (radius: 25)
[06:12:44 -203041.695132] Model parameter optimization (eps = 0.100000)

[06:12:52] ML tree search #7, logLikelihood: -203041.516786

[06:12:52 -735831.175139] Initial branch length optimization
[06:12:54 -650315.808267] Model parameter optimization (eps = 10.000000)
[06:13:27 -648487.741450] AUTODETECT spr round 1 (radius: 5)
[06:15:33 -529729.261820] AUTODETECT spr round 2 (radius: 10)
[06:17:57 -329713.360492] AUTODETECT spr round 3 (radius: 15)
[06:20:25 -253927.340159] AUTODETECT spr round 4 (radius: 20)
[06:23:33 -232624.216621] AUTODETECT spr round 5 (radius: 25)
[06:27:08 -231858.730110] SPR radius for FAST iterations: 25 (autodetect)
[06:27:08 -231858.730110] Model parameter optimization (eps = 3.000000)
[06:27:27 -231620.775529] FAST spr round 1 (radius: 25)
[06:29:35 -204044.047538] FAST spr round 2 (radius: 25)
[06:31:22 -203196.315092] FAST spr round 3 (radius: 25)
[06:33:09 -203136.391101] FAST spr round 4 (radius: 25)
[06:34:44 -203131.404706] FAST spr round 5 (radius: 25)
[06:36:18 -203131.404380] Model parameter optimization (eps = 1.000000)
[06:36:32 -203129.029132] SLOW spr round 1 (radius: 5)
[06:38:37 -203055.080692] SLOW spr round 2 (radius: 5)
[06:40:41 -203042.623939] SLOW spr round 3 (radius: 5)
[06:42:41 -203040.103475] SLOW spr round 4 (radius: 5)
[06:44:38 -203040.103054] SLOW spr round 5 (radius: 10)
[06:46:40 -203040.102786] SLOW spr round 6 (radius: 15)
[06:50:48 -203035.375993] SLOW spr round 7 (radius: 5)
[06:53:13 -203029.613380] SLOW spr round 8 (radius: 5)
[06:55:25 -203029.347417] SLOW spr round 9 (radius: 5)
[06:57:26 -203029.347395] SLOW spr round 10 (radius: 10)
[06:59:29 -203029.347395] SLOW spr round 11 (radius: 15)
[07:03:30 -203029.347395] SLOW spr round 12 (radius: 20)
[07:09:05 -203029.347395] SLOW spr round 13 (radius: 25)
[07:14:29 -203029.347395] Model parameter optimization (eps = 0.100000)

[07:14:42] ML tree search #8, logLikelihood: -203027.401120

[07:14:42 -734637.073002] Initial branch length optimization
[07:14:44 -649771.999174] Model parameter optimization (eps = 10.000000)
[07:15:10 -648007.455198] AUTODETECT spr round 1 (radius: 5)
[07:17:14 -523231.805174] AUTODETECT spr round 2 (radius: 10)
[07:19:43 -333864.559822] AUTODETECT spr round 3 (radius: 15)
[07:22:11 -252333.486657] AUTODETECT spr round 4 (radius: 20)
[07:24:51 -235775.932022] AUTODETECT spr round 5 (radius: 25)
[07:27:54 -234726.494363] SPR radius for FAST iterations: 25 (autodetect)
[07:27:54 -234726.494363] Model parameter optimization (eps = 3.000000)
[07:28:18 -234443.256021] FAST spr round 1 (radius: 25)
[07:32:19 -204263.688544] FAST spr round 2 (radius: 25)
[07:35:00 -203233.107468] FAST spr round 3 (radius: 25)
[07:36:44 -203184.905028] FAST spr round 4 (radius: 25)
[07:38:18 -203174.518368] FAST spr round 5 (radius: 25)
[07:39:50 -203174.518339] Model parameter optimization (eps = 1.000000)
[07:40:02 -203169.959478] SLOW spr round 1 (radius: 5)
[07:42:06 -203102.477298] SLOW spr round 2 (radius: 5)
[07:44:07 -203083.910765] SLOW spr round 3 (radius: 5)
[07:46:03 -203082.832701] SLOW spr round 4 (radius: 5)
[07:47:57 -203082.832700] SLOW spr round 5 (radius: 10)
[07:49:58 -203081.708951] SLOW spr round 6 (radius: 5)
[07:52:20 -203079.834697] SLOW spr round 7 (radius: 5)
[07:54:29 -203079.834688] SLOW spr round 8 (radius: 10)
[07:56:37 -203079.834688] SLOW spr round 9 (radius: 15)
[08:00:51 -203079.834688] SLOW spr round 10 (radius: 20)
[08:07:10 -203079.834688] SLOW spr round 11 (radius: 25)
[08:13:23 -203079.834688] Model parameter optimization (eps = 0.100000)

[08:13:36] ML tree search #9, logLikelihood: -203078.687641

[08:13:36 -736044.419539] Initial branch length optimization
[08:13:38 -649390.756583] Model parameter optimization (eps = 10.000000)
[08:14:03 -647509.098724] AUTODETECT spr round 1 (radius: 5)
[08:16:08 -528928.906555] AUTODETECT spr round 2 (radius: 10)
[08:18:36 -330949.150681] AUTODETECT spr round 3 (radius: 15)
[08:21:11 -245247.947478] AUTODETECT spr round 4 (radius: 20)
[08:24:19 -234792.051701] AUTODETECT spr round 5 (radius: 25)
[08:27:42 -233606.696609] SPR radius for FAST iterations: 25 (autodetect)
[08:27:42 -233606.696609] Model parameter optimization (eps = 3.000000)
[08:28:04 -233273.796628] FAST spr round 1 (radius: 25)
[08:30:22 -204397.015689] FAST spr round 2 (radius: 25)
[08:32:20 -203244.924394] FAST spr round 3 (radius: 25)
[08:34:06 -203182.583627] FAST spr round 4 (radius: 25)
[08:35:44 -203155.734231] FAST spr round 5 (radius: 25)
[08:37:18 -203154.750313] FAST spr round 6 (radius: 25)
[08:38:49 -203154.750024] Model parameter optimization (eps = 1.000000)
[08:39:01 -203137.850666] SLOW spr round 1 (radius: 5)
[08:41:04 -203057.757251] SLOW spr round 2 (radius: 5)
[08:43:04 -203057.036149] SLOW spr round 3 (radius: 5)
[08:44:58 -203057.035918] SLOW spr round 4 (radius: 10)
[08:46:59 -203057.035914] SLOW spr round 5 (radius: 15)
[08:51:06 -203057.035913] SLOW spr round 6 (radius: 20)
[08:56:50 -203057.035913] SLOW spr round 7 (radius: 25)
[09:02:36 -203057.035913] Model parameter optimization (eps = 0.100000)

[09:02:45] ML tree search #10, logLikelihood: -203056.521613

[09:02:45 -733217.603157] Initial branch length optimization
[09:02:48 -648395.863653] Model parameter optimization (eps = 10.000000)
[09:03:19 -646565.211768] AUTODETECT spr round 1 (radius: 5)
[09:05:24 -526462.664035] AUTODETECT spr round 2 (radius: 10)
[09:07:46 -324011.397843] AUTODETECT spr round 3 (radius: 15)
[09:10:10 -249754.865377] AUTODETECT spr round 4 (radius: 20)
[09:13:14 -237356.433498] AUTODETECT spr round 5 (radius: 25)
[09:16:37 -236950.456593] SPR radius for FAST iterations: 25 (autodetect)
[09:16:37 -236950.456593] Model parameter optimization (eps = 3.000000)
[09:17:04 -236698.903341] FAST spr round 1 (radius: 25)
[09:19:22 -204979.917642] FAST spr round 2 (radius: 25)
[09:21:18 -203379.994428] FAST spr round 3 (radius: 25)
[09:23:07 -203168.116478] FAST spr round 4 (radius: 25)
[09:24:47 -203157.705525] FAST spr round 5 (radius: 25)
[09:26:23 -203155.453967] FAST spr round 6 (radius: 25)
[09:27:59 -203155.453936] Model parameter optimization (eps = 1.000000)
[09:28:12 -203150.265772] SLOW spr round 1 (radius: 5)
[09:30:23 -203071.145002] SLOW spr round 2 (radius: 5)
[09:32:28 -203063.743217] SLOW spr round 3 (radius: 5)
[09:34:28 -203063.243803] SLOW spr round 4 (radius: 5)
[09:36:26 -203063.243740] SLOW spr round 5 (radius: 10)
[09:38:33 -203059.122671] SLOW spr round 6 (radius: 5)
[09:41:01 -203048.984502] SLOW spr round 7 (radius: 5)
[09:43:07 -203048.204283] SLOW spr round 8 (radius: 5)
[09:45:06 -203047.577167] SLOW spr round 9 (radius: 5)
[09:47:02 -203047.576801] SLOW spr round 10 (radius: 10)
[09:49:03 -203047.576788] SLOW spr round 11 (radius: 15)
[09:53:06 -203047.576788] SLOW spr round 12 (radius: 20)
[09:58:34 -203047.576788] SLOW spr round 13 (radius: 25)
[10:03:58 -203047.576788] Model parameter optimization (eps = 0.100000)

[10:04:09] ML tree search #11, logLikelihood: -203046.923014

[10:04:09 -738477.546635] Initial branch length optimization
[10:04:11 -652084.493125] Model parameter optimization (eps = 10.000000)
[10:04:44 -650211.644765] AUTODETECT spr round 1 (radius: 5)
[10:06:48 -524781.270506] AUTODETECT spr round 2 (radius: 10)
[10:09:06 -330043.739464] AUTODETECT spr round 3 (radius: 15)
[10:11:38 -247701.692380] AUTODETECT spr round 4 (radius: 20)
[10:14:43 -235330.709834] AUTODETECT spr round 5 (radius: 25)
[10:18:05 -235245.321520] SPR radius for FAST iterations: 25 (autodetect)
[10:18:05 -235245.321520] Model parameter optimization (eps = 3.000000)
[10:18:21 -235014.025104] FAST spr round 1 (radius: 25)
[10:20:30 -204818.487702] FAST spr round 2 (radius: 25)
[10:22:23 -203284.985862] FAST spr round 3 (radius: 25)
[10:24:07 -203169.940327] FAST spr round 4 (radius: 25)
[10:25:43 -203145.685298] FAST spr round 5 (radius: 25)
[10:27:18 -203139.136041] FAST spr round 6 (radius: 25)
[10:28:50 -203139.135988] Model parameter optimization (eps = 1.000000)
[10:29:05 -203120.826855] SLOW spr round 1 (radius: 5)
[10:31:09 -203075.322599] SLOW spr round 2 (radius: 5)
[10:33:07 -203073.015756] SLOW spr round 3 (radius: 5)
[10:35:02 -203072.703578] SLOW spr round 4 (radius: 5)
[10:36:56 -203072.703033] SLOW spr round 5 (radius: 10)
[10:38:58 -203069.081148] SLOW spr round 6 (radius: 5)
[10:41:19 -203065.325259] SLOW spr round 7 (radius: 5)
[10:43:22 -203065.324336] SLOW spr round 8 (radius: 10)
[10:45:26 -203065.323762] SLOW spr round 9 (radius: 15)
[10:49:31 -203065.323197] SLOW spr round 10 (radius: 20)
[10:55:26 -203065.322633] SLOW spr round 11 (radius: 25)
[11:01:11 -203065.322069] Model parameter optimization (eps = 0.100000)

[11:01:16] ML tree search #12, logLikelihood: -203065.226809

[11:01:16 -737134.659011] Initial branch length optimization
[11:01:19 -651426.929100] Model parameter optimization (eps = 10.000000)
[11:01:50 -649524.192830] AUTODETECT spr round 1 (radius: 5)
[11:03:58 -527777.315161] AUTODETECT spr round 2 (radius: 10)
[11:06:24 -351576.987894] AUTODETECT spr round 3 (radius: 15)
[11:08:54 -263566.954884] AUTODETECT spr round 4 (radius: 20)
[11:12:02 -241932.700343] AUTODETECT spr round 5 (radius: 25)
[11:15:38 -240405.797080] SPR radius for FAST iterations: 25 (autodetect)
[11:15:38 -240405.797080] Model parameter optimization (eps = 3.000000)
[11:16:00 -240115.265304] FAST spr round 1 (radius: 25)
[11:18:14 -204596.523107] FAST spr round 2 (radius: 25)
[11:20:04 -203243.571355] FAST spr round 3 (radius: 25)
[11:21:49 -203127.509792] FAST spr round 4 (radius: 25)
[11:23:25 -203121.117645] FAST spr round 5 (radius: 25)
[11:24:59 -203118.234844] FAST spr round 6 (radius: 25)
[11:26:32 -203118.234499] Model parameter optimization (eps = 1.000000)
[11:26:46 -203114.127206] SLOW spr round 1 (radius: 5)
[11:28:49 -203050.446224] SLOW spr round 2 (radius: 5)
[11:30:50 -203043.605079] SLOW spr round 3 (radius: 5)
[11:32:49 -203042.323057] SLOW spr round 4 (radius: 5)
[11:34:43 -203042.322835] SLOW spr round 5 (radius: 10)
[11:36:43 -203042.322626] SLOW spr round 6 (radius: 15)
[11:40:48 -203042.322417] SLOW spr round 7 (radius: 20)
[11:46:23 -203042.322208] SLOW spr round 8 (radius: 25)
[11:51:44 -203042.321999] Model parameter optimization (eps = 0.100000)

[11:51:51] ML tree search #13, logLikelihood: -203041.972389

[11:51:51 -732468.777164] Initial branch length optimization
[11:51:53 -647807.153281] Model parameter optimization (eps = 10.000000)
[11:52:19 -646052.585483] AUTODETECT spr round 1 (radius: 5)
[11:54:24 -522412.908448] AUTODETECT spr round 2 (radius: 10)
[11:56:39 -336286.749605] AUTODETECT spr round 3 (radius: 15)
[11:59:01 -257110.827496] AUTODETECT spr round 4 (radius: 20)
[12:01:45 -240099.011278] AUTODETECT spr round 5 (radius: 25)
[12:04:52 -237665.828019] SPR radius for FAST iterations: 25 (autodetect)
[12:04:52 -237665.828019] Model parameter optimization (eps = 3.000000)
[12:05:09 -237403.767702] FAST spr round 1 (radius: 25)
[12:07:18 -204463.872802] FAST spr round 2 (radius: 25)
[12:09:10 -203226.057262] FAST spr round 3 (radius: 25)
[12:10:55 -203141.580162] FAST spr round 4 (radius: 25)
[12:12:31 -203129.340057] FAST spr round 5 (radius: 25)
[12:14:03 -203129.339861] Model parameter optimization (eps = 1.000000)
[12:14:14 -203127.218893] SLOW spr round 1 (radius: 5)
[12:16:18 -203084.725631] SLOW spr round 2 (radius: 5)
[12:18:16 -203082.098614] SLOW spr round 3 (radius: 5)
[12:20:12 -203082.098584] SLOW spr round 4 (radius: 10)
[12:22:13 -203082.098271] SLOW spr round 5 (radius: 15)
[12:26:25 -203082.098271] SLOW spr round 6 (radius: 20)
[12:32:10 -203082.098271] SLOW spr round 7 (radius: 25)
[12:37:34 -203082.098270] Model parameter optimization (eps = 0.100000)

[12:37:39] ML tree search #14, logLikelihood: -203082.085587

[12:37:39 -738809.172763] Initial branch length optimization
[12:37:41 -651756.620782] Model parameter optimization (eps = 10.000000)
[12:38:09 -649897.426296] AUTODETECT spr round 1 (radius: 5)
[12:40:17 -528291.882995] AUTODETECT spr round 2 (radius: 10)
[12:42:58 -315217.234690] AUTODETECT spr round 3 (radius: 15)
[12:45:26 -252617.252464] AUTODETECT spr round 4 (radius: 20)
[12:48:41 -238031.224459] AUTODETECT spr round 5 (radius: 25)
[12:52:04 -236821.459368] SPR radius for FAST iterations: 25 (autodetect)
[12:52:04 -236821.459368] Model parameter optimization (eps = 3.000000)
[12:52:24 -236564.210055] FAST spr round 1 (radius: 25)
[12:54:34 -204185.152401] FAST spr round 2 (radius: 25)
[12:56:27 -203268.019814] FAST spr round 3 (radius: 25)
[12:58:15 -203143.753648] FAST spr round 4 (radius: 25)
[12:59:52 -203139.550830] FAST spr round 5 (radius: 25)
[13:01:25 -203139.550691] Model parameter optimization (eps = 1.000000)
[13:01:39 -203135.883212] SLOW spr round 1 (radius: 5)
[13:03:44 -203060.115070] SLOW spr round 2 (radius: 5)
[13:05:45 -203059.268363] SLOW spr round 3 (radius: 5)
[13:07:39 -203059.267505] SLOW spr round 4 (radius: 10)
[13:09:41 -203057.184115] SLOW spr round 5 (radius: 5)
[13:11:58 -203057.183479] SLOW spr round 6 (radius: 10)
[13:14:12 -203057.182944] SLOW spr round 7 (radius: 15)
[13:17:59 -203057.182411] SLOW spr round 8 (radius: 20)
[13:23:37 -203057.181877] SLOW spr round 9 (radius: 25)
[13:29:03 -203057.181343] Model parameter optimization (eps = 0.100000)

[13:29:12] ML tree search #15, logLikelihood: -203057.032872

[13:29:12 -738446.504534] Initial branch length optimization
[13:29:14 -651960.939125] Model parameter optimization (eps = 10.000000)
[13:29:42 -650050.153281] AUTODETECT spr round 1 (radius: 5)
[13:31:48 -520174.204363] AUTODETECT spr round 2 (radius: 10)
[13:34:05 -357216.673225] AUTODETECT spr round 3 (radius: 15)
[13:36:33 -257352.658547] AUTODETECT spr round 4 (radius: 20)
[13:39:33 -240282.601683] AUTODETECT spr round 5 (radius: 25)
[13:42:56 -237751.715661] SPR radius for FAST iterations: 25 (autodetect)
[13:42:56 -237751.715661] Model parameter optimization (eps = 3.000000)
[13:43:17 -237541.674447] FAST spr round 1 (radius: 25)
[13:45:30 -204371.850379] FAST spr round 2 (radius: 25)
[13:47:20 -203275.677605] FAST spr round 3 (radius: 25)
[13:49:00 -203164.312661] FAST spr round 4 (radius: 25)
[13:50:37 -203138.505017] FAST spr round 5 (radius: 25)
[13:52:10 -203138.038557] FAST spr round 6 (radius: 25)
[13:53:42 -203138.038317] Model parameter optimization (eps = 1.000000)
[13:53:55 -203126.744716] SLOW spr round 1 (radius: 5)
[13:55:59 -203065.888204] SLOW spr round 2 (radius: 5)
[13:57:57 -203063.897744] SLOW spr round 3 (radius: 5)
[13:59:55 -203063.897348] SLOW spr round 4 (radius: 10)
[14:01:59 -203063.896976] SLOW spr round 5 (radius: 15)
[14:06:14 -203063.896606] SLOW spr round 6 (radius: 20)
[14:12:15 -203063.896464] SLOW spr round 7 (radius: 25)
[14:18:19 -203063.896461] Model parameter optimization (eps = 0.100000)

[14:18:24] ML tree search #16, logLikelihood: -203063.842804

[14:18:24 -735809.056665] Initial branch length optimization
[14:18:27 -649840.937163] Model parameter optimization (eps = 10.000000)
[14:18:51 -648078.661465] AUTODETECT spr round 1 (radius: 5)
[14:20:58 -533092.908847] AUTODETECT spr round 2 (radius: 10)
[14:23:31 -341728.901174] AUTODETECT spr round 3 (radius: 15)
[14:26:05 -253663.347756] AUTODETECT spr round 4 (radius: 20)
[14:29:15 -241756.840293] AUTODETECT spr round 5 (radius: 25)
[14:32:52 -238934.500250] SPR radius for FAST iterations: 25 (autodetect)
[14:32:52 -238934.500250] Model parameter optimization (eps = 3.000000)
[14:33:14 -238626.855538] FAST spr round 1 (radius: 25)
[14:35:28 -204481.982130] FAST spr round 2 (radius: 25)
[14:37:16 -203241.513981] FAST spr round 3 (radius: 25)
[14:38:57 -203158.588746] FAST spr round 4 (radius: 25)
[14:40:29 -203149.332188] FAST spr round 5 (radius: 25)
[14:42:00 -203145.310745] FAST spr round 6 (radius: 25)
[14:43:30 -203145.310373] Model parameter optimization (eps = 1.000000)
[14:43:46 -203140.810343] SLOW spr round 1 (radius: 5)
[14:45:46 -203070.339970] SLOW spr round 2 (radius: 5)
[14:47:42 -203066.150019] SLOW spr round 3 (radius: 5)
[14:49:35 -203065.967019] SLOW spr round 4 (radius: 5)
[14:51:27 -203065.966422] SLOW spr round 5 (radius: 10)
[14:53:25 -203065.966204] SLOW spr round 6 (radius: 15)
[14:57:33 -203065.966200] SLOW spr round 7 (radius: 20)
[15:03:26 -203065.966200] SLOW spr round 8 (radius: 25)
[15:09:16 -203065.966200] Model parameter optimization (eps = 0.100000)

[15:09:20] ML tree search #17, logLikelihood: -203065.874353

[15:09:20 -738497.838502] Initial branch length optimization
[15:09:22 -652133.183638] Model parameter optimization (eps = 10.000000)
[15:09:48 -650291.333443] AUTODETECT spr round 1 (radius: 5)
[15:11:52 -520447.605509] AUTODETECT spr round 2 (radius: 10)
[15:14:11 -325603.733101] AUTODETECT spr round 3 (radius: 15)
[15:16:35 -243957.663873] AUTODETECT spr round 4 (radius: 20)
[15:19:34 -229294.292559] AUTODETECT spr round 5 (radius: 25)
[15:22:51 -228119.779181] SPR radius for FAST iterations: 25 (autodetect)
[15:22:51 -228119.779181] Model parameter optimization (eps = 3.000000)
[15:23:08 -227829.937078] FAST spr round 1 (radius: 25)
[15:25:19 -203881.724120] FAST spr round 2 (radius: 25)
[15:27:10 -203220.942577] FAST spr round 3 (radius: 25)
[15:28:55 -203167.364478] FAST spr round 4 (radius: 25)
[15:30:32 -203162.947190] FAST spr round 5 (radius: 25)
[15:32:09 -203159.538485] FAST spr round 6 (radius: 25)
[15:33:44 -203159.537919] Model parameter optimization (eps = 1.000000)
[15:33:55 -203150.990920] SLOW spr round 1 (radius: 5)
[15:36:00 -203083.799705] SLOW spr round 2 (radius: 5)
[15:38:02 -203082.616489] SLOW spr round 3 (radius: 5)
[15:40:01 -203082.616488] SLOW spr round 4 (radius: 10)
[15:42:05 -203082.616488] SLOW spr round 5 (radius: 15)
[15:46:24 -203082.616488] SLOW spr round 6 (radius: 20)
[15:52:22 -203082.616487] SLOW spr round 7 (radius: 25)
[15:57:48 -203082.616487] Model parameter optimization (eps = 0.100000)

[15:57:53] ML tree search #18, logLikelihood: -203082.582975

[15:57:53 -736580.737921] Initial branch length optimization
[15:57:55 -650344.405503] Model parameter optimization (eps = 10.000000)
[15:58:21 -648435.191136] AUTODETECT spr round 1 (radius: 5)
[16:00:29 -531229.355678] AUTODETECT spr round 2 (radius: 10)
[16:02:57 -353662.317740] AUTODETECT spr round 3 (radius: 15)
[16:05:23 -263608.261511] AUTODETECT spr round 4 (radius: 20)
[16:08:15 -242705.268182] AUTODETECT spr round 5 (radius: 25)
[16:11:42 -240386.605156] SPR radius for FAST iterations: 25 (autodetect)
[16:11:42 -240386.605156] Model parameter optimization (eps = 3.000000)
[16:12:00 -240105.762973] FAST spr round 1 (radius: 25)
[16:14:09 -204413.162780] FAST spr round 2 (radius: 25)
[16:16:00 -203228.354263] FAST spr round 3 (radius: 25)
[16:17:43 -203130.024646] FAST spr round 4 (radius: 25)
[16:19:17 -203109.108425] FAST spr round 5 (radius: 25)
[16:20:49 -203109.108124] Model parameter optimization (eps = 1.000000)
[16:20:55 -203108.858820] SLOW spr round 1 (radius: 5)
[16:23:01 -203067.275936] SLOW spr round 2 (radius: 5)
[16:24:57 -203064.935020] SLOW spr round 3 (radius: 5)
[16:26:53 -203064.119885] SLOW spr round 4 (radius: 5)
[16:28:45 -203064.119463] SLOW spr round 5 (radius: 10)
[16:30:46 -203063.271668] SLOW spr round 6 (radius: 5)
[16:33:04 -203055.920831] SLOW spr round 7 (radius: 5)
[16:35:05 -203055.920755] SLOW spr round 8 (radius: 10)
[16:37:08 -203055.920755] SLOW spr round 9 (radius: 15)
[16:41:17 -203055.920755] SLOW spr round 10 (radius: 20)
[16:47:09 -203055.920755] SLOW spr round 11 (radius: 25)
[16:52:47 -203055.920755] Model parameter optimization (eps = 0.100000)

[16:52:59] ML tree search #19, logLikelihood: -203055.588059

[16:52:59 -737509.237524] Initial branch length optimization
[16:53:01 -650016.877648] Model parameter optimization (eps = 10.000000)
[16:53:37 -648238.208354] AUTODETECT spr round 1 (radius: 5)
[16:55:43 -533310.473311] AUTODETECT spr round 2 (radius: 10)
[16:58:25 -335738.581281] AUTODETECT spr round 3 (radius: 15)
[17:01:04 -249944.778063] AUTODETECT spr round 4 (radius: 20)
[17:04:12 -238701.851687] AUTODETECT spr round 5 (radius: 25)
[17:07:36 -235835.632109] SPR radius for FAST iterations: 25 (autodetect)
[17:07:36 -235835.632109] Model parameter optimization (eps = 3.000000)
[17:07:57 -235559.335077] FAST spr round 1 (radius: 25)
[17:10:11 -204262.455008] FAST spr round 2 (radius: 25)
[17:12:03 -203265.534522] FAST spr round 3 (radius: 25)
[17:13:49 -203169.455922] FAST spr round 4 (radius: 25)
[17:15:27 -203150.451116] FAST spr round 5 (radius: 25)
[17:17:03 -203150.450837] Model parameter optimization (eps = 1.000000)
[17:17:19 -203146.424803] SLOW spr round 1 (radius: 5)
[17:19:26 -203084.746974] SLOW spr round 2 (radius: 5)
[17:21:29 -203082.054879] SLOW spr round 3 (radius: 5)
[17:23:26 -203082.054741] SLOW spr round 4 (radius: 10)
[17:25:31 -203078.972699] SLOW spr round 5 (radius: 5)
[17:27:52 -203078.365089] SLOW spr round 6 (radius: 5)
[17:29:59 -203078.365087] SLOW spr round 7 (radius: 10)
[17:32:06 -203078.365087] SLOW spr round 8 (radius: 15)
[17:36:09 -203078.365087] SLOW spr round 9 (radius: 20)
[17:41:51 -203078.365087] SLOW spr round 10 (radius: 25)
[17:47:09 -203078.365087] Model parameter optimization (eps = 0.100000)

[17:47:14] ML tree search #20, logLikelihood: -203078.346703


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.176772,0.487686) (0.171573,0.774069) (0.361941,0.954969) (0.289714,1.502650) 
   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: -203027.401120

AIC score: 410064.802240 / AICc score: 8454124.802240 / BIC score: 418836.727004
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=587).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 127 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JC4/3_mltree/Q96JC4.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JC4/3_mltree/Q96JC4.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JC4/3_mltree/Q96JC4.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JC4/3_mltree/Q96JC4.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96JC4/3_mltree/Q96JC4.raxml.log

Analysis started: 01-Jul-2021 10:25:32 / finished: 02-Jul-2021 04:12:46

Elapsed time: 64034.371 seconds

Consumed energy: 5333.591 Wh (= 27 km in an electric car, or 133 km with an e-scooter!)