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 13:05:14 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14807/2_msa/Q14807_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14807/3_mltree/Q14807 --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/Q14807/2_msa/Q14807_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 464 sites

WARNING: Sequences tr_J3KJS4_J3KJS4_COCIM_246410 and tr_A0A0J6Y1X8_A0A0J6Y1X8_COCIT_404692 are exactly identical!
WARNING: Sequences tr_D8R093_D8R093_SELML_88036 and tr_D8SZN8_D8SZN8_SELML_88036 are exactly identical!
WARNING: Sequences tr_D8RFB1_D8RFB1_SELML_88036 and tr_D8SDG4_D8SDG4_SELML_88036 are exactly identical!
WARNING: Sequences tr_G3QE28_G3QE28_GORGO_9595 and tr_H2Q3C0_H2Q3C0_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QE28_G3QE28_GORGO_9595 and sp_Q8NI77_KI18A_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QE28_G3QE28_GORGO_9595 and tr_A0A2R9B2F7_A0A2R9B2F7_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A179U9J4_A0A179U9J4_BLAGS_559298 and tr_C5GW44_C5GW44_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_F9FKN3_F9FKN3_FUSOF_660025 and tr_A0A0D2XVS4_A0A0D2XVS4_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_F9FKN3_F9FKN3_FUSOF_660025 and tr_N4TZI7_N4TZI7_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9FKN3_F9FKN3_FUSOF_660025 and tr_X0CT34_X0CT34_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_A0A158NT00_A0A158NT00_ATTCE_12957 and tr_A0A151I4P3_A0A151I4P3_9HYME_520822 are exactly identical!
WARNING: Sequences tr_Q2ULH9_Q2ULH9_ASPOR_510516 and tr_A0A1S9DN55_A0A1S9DN55_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A0E0HFJ7_A0A0E0HFJ7_ORYNI_4536 and tr_B8AYZ9_B8AYZ9_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0HFJ7_A0A0E0HFJ7_ORYNI_4536 and tr_A0A0E0PNJ0_A0A0E0PNJ0_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0HFJ7_A0A0E0HFJ7_ORYNI_4536 and sp_Q6L512_KN10C_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A2QSG5_A2QSG5_ASPNC_425011 and tr_G3YFT9_G3YFT9_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2QSG5_A2QSG5_ASPNC_425011 and tr_A0A318ZYM9_A0A318ZYM9_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_F6YBJ5_F6YBJ5_MACMU_9544 and tr_G7Q0V0_G7Q0V0_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G7XLY5_G7XLY5_ASPKW_1033177 and tr_A0A146FA68_A0A146FA68_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_F9XDP7_F9XDP7_ZYMTI_336722 and tr_A0A1X7RWM3_A0A1X7RWM3_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_F2SF99_F2SF99_TRIRC_559305 and tr_A0A178EU63_A0A178EU63_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_C4V919_C4V919_NOSCE_578460 and tr_A0A0F9WAA3_A0A0F9WAA3_9MICR_40302 are exactly identical!
WARNING: Sequences tr_W2PPA8_W2PPA8_PHYPN_761204 and tr_A0A0W8D6C7_A0A0W8D6C7_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2PPA8_W2PPA8_PHYPN_761204 and tr_W2KCI8_W2KCI8_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_W2Q0C1_W2Q0C1_PHYPN_761204 and tr_A0A0W8DVX0_A0A0W8DVX0_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2Q0C1_W2Q0C1_PHYPN_761204 and tr_W2KWS8_W2KWS8_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A096NFN0_A0A096NFN0_PAPAN_9555 and tr_A0A2K5LN97_A0A2K5LN97_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096NFN0_A0A096NFN0_PAPAN_9555 and tr_A0A2K6CRD7_A0A2K6CRD7_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A078JAN7_A0A078JAN7_BRANA_3708 and tr_A0A0D3EIC4_A0A0D3EIC4_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A094GIE0_A0A094GIE0_9PEZI_1420912 and tr_A0A2P2SWM1_A0A2P2SWM1_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_I1RQJ0_I1RQJ0_GIBZE_229533 and tr_A0A2T4GLJ8_A0A2T4GLJ8_FUSCU_5516 are exactly identical!
WARNING: Sequences tr_A0A1S4BDX3_A0A1S4BDX3_TOBAC_4097 and tr_A0A1U7VQJ6_A0A1U7VQJ6_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4BMR9_A0A1S4BMR9_TOBAC_4097 and tr_A0A1U7Y9T6_A0A1U7Y9T6_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1Q3DXK1_A0A1Q3DXK1_LENED_5353 and tr_A0A1Q3DXK8_A0A1Q3DXK8_LENED_5353 are exactly identical!
WARNING: Sequences tr_A0A1Q3DXK1_A0A1Q3DXK1_LENED_5353 and tr_A0A1Q3DY15_A0A1Q3DY15_LENED_5353 are exactly identical!
WARNING: Sequences tr_A0A2D0S606_A0A2D0S606_ICTPU_7998 and tr_A0A2D0S624_A0A2D0S624_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0S606_A0A2D0S606_ICTPU_7998 and tr_A0A2D0S6W4_A0A2D0S6W4_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2D0S606_A0A2D0S606_ICTPU_7998 and tr_A0A2D0S7G8_A0A2D0S7G8_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2K5M0W1_A0A2K5M0W1_CERAT_9531 and tr_A0A2K5ZLU3_A0A2K5ZLU3_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2K6EA63_A0A2K6EA63_MACNE_9545 and tr_A0A2K6ABS2_A0A2K6ABS2_MANLE_9568 are exactly identical!
WARNING: Duplicate sequences found: 40

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/Q14807/3_mltree/Q14807.raxml.reduced.phy

Alignment comprises 1 partitions and 464 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 464 / 464
Gaps: 7.56 %
Invariant sites: 1.29 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14807/3_mltree/Q14807.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 / 67 / 5360
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -858920.419805] Initial branch length optimization
[00:00:03 -710895.857643] Model parameter optimization (eps = 10.000000)
[00:00:23 -710327.101796] AUTODETECT spr round 1 (radius: 5)
[00:01:51 -504764.332421] AUTODETECT spr round 2 (radius: 10)
[00:03:35 -373611.429803] AUTODETECT spr round 3 (radius: 15)
[00:05:28 -305785.657133] AUTODETECT spr round 4 (radius: 20)
[00:07:30 -260549.093461] AUTODETECT spr round 5 (radius: 25)
[00:09:33 -252062.961915] SPR radius for FAST iterations: 25 (autodetect)
[00:09:33 -252062.961915] Model parameter optimization (eps = 3.000000)
[00:09:38 -252059.900880] FAST spr round 1 (radius: 25)
[00:11:21 -220268.518025] FAST spr round 2 (radius: 25)
[00:12:49 -219041.411110] FAST spr round 3 (radius: 25)
[00:14:06 -218976.590597] FAST spr round 4 (radius: 25)
[00:15:19 -218963.468543] FAST spr round 5 (radius: 25)
[00:16:28 -218963.468450] Model parameter optimization (eps = 1.000000)
[00:16:39 -218923.378599] SLOW spr round 1 (radius: 5)
[00:18:17 -218859.673695] SLOW spr round 2 (radius: 5)
[00:19:47 -218853.741398] SLOW spr round 3 (radius: 5)
[00:21:16 -218852.307958] SLOW spr round 4 (radius: 5)
[00:22:44 -218852.307639] SLOW spr round 5 (radius: 10)
[00:24:13 -218850.142022] SLOW spr round 6 (radius: 5)
[00:26:00 -218848.564574] SLOW spr round 7 (radius: 5)
[00:27:32 -218848.564570] SLOW spr round 8 (radius: 10)
[00:29:05 -218848.064575] SLOW spr round 9 (radius: 5)
[00:30:49 -218847.934150] SLOW spr round 10 (radius: 5)
[00:32:32 -218847.934122] SLOW spr round 11 (radius: 10)
[00:34:16 -218847.934122] SLOW spr round 12 (radius: 15)
[00:36:52 -218838.482179] SLOW spr round 13 (radius: 5)
[00:38:58 -218837.627224] SLOW spr round 14 (radius: 5)
[00:40:49 -218837.627206] SLOW spr round 15 (radius: 10)
[00:42:34 -218837.627206] SLOW spr round 16 (radius: 15)
[00:45:06 -218837.627206] SLOW spr round 17 (radius: 20)
[00:49:04 -218837.627206] SLOW spr round 18 (radius: 25)
[00:53:59 -218837.627206] Model parameter optimization (eps = 0.100000)

[00:54:05] ML tree search #1, logLikelihood: -218837.535883

[00:54:05 -860912.882203] Initial branch length optimization
[00:54:07 -715849.565520] Model parameter optimization (eps = 10.000000)
[00:54:31 -715428.917563] AUTODETECT spr round 1 (radius: 5)
[00:56:14 -502322.204429] AUTODETECT spr round 2 (radius: 10)
[00:58:07 -372466.323106] AUTODETECT spr round 3 (radius: 15)
[01:00:07 -292291.227683] AUTODETECT spr round 4 (radius: 20)
[01:02:10 -262677.032470] AUTODETECT spr round 5 (radius: 25)
[01:04:30 -259018.804342] SPR radius for FAST iterations: 25 (autodetect)
[01:04:30 -259018.804342] Model parameter optimization (eps = 3.000000)
[01:04:44 -258921.039065] FAST spr round 1 (radius: 25)
[01:06:43 -221149.601077] FAST spr round 2 (radius: 25)
[01:08:21 -219201.048006] FAST spr round 3 (radius: 25)
[01:09:48 -218949.834016] FAST spr round 4 (radius: 25)
[01:11:09 -218933.671320] FAST spr round 5 (radius: 25)
[01:12:28 -218926.247951] FAST spr round 6 (radius: 25)
[01:13:45 -218926.247194] Model parameter optimization (eps = 1.000000)
[01:13:51 -218925.730449] SLOW spr round 1 (radius: 5)
[01:15:37 -218883.101984] SLOW spr round 2 (radius: 5)
[01:17:21 -218844.692374] SLOW spr round 3 (radius: 5)
[01:19:00 -218839.302929] SLOW spr round 4 (radius: 5)
[01:20:38 -218838.277074] SLOW spr round 5 (radius: 5)
[01:22:15 -218838.277074] SLOW spr round 6 (radius: 10)
[01:23:56 -218836.442280] SLOW spr round 7 (radius: 5)
[01:25:57 -218834.876783] SLOW spr round 8 (radius: 5)
[01:27:45 -218834.876781] SLOW spr round 9 (radius: 10)
[01:29:31 -218834.797168] SLOW spr round 10 (radius: 15)
[01:32:07 -218834.796476] SLOW spr round 11 (radius: 20)
[01:36:05 -218834.796473] SLOW spr round 12 (radius: 25)
[01:40:51 -218834.796473] Model parameter optimization (eps = 0.100000)

[01:41:01] ML tree search #2, logLikelihood: -218833.952632

[01:41:01 -860885.411400] Initial branch length optimization
[01:41:03 -713498.689120] Model parameter optimization (eps = 10.000000)
[01:41:23 -713054.820918] AUTODETECT spr round 1 (radius: 5)
[01:43:01 -502848.885580] AUTODETECT spr round 2 (radius: 10)
[01:44:54 -378102.014557] AUTODETECT spr round 3 (radius: 15)
[01:46:59 -299116.464494] AUTODETECT spr round 4 (radius: 20)
[01:49:16 -265456.871801] AUTODETECT spr round 5 (radius: 25)
[01:51:23 -258326.238337] SPR radius for FAST iterations: 25 (autodetect)
[01:51:23 -258326.238337] Model parameter optimization (eps = 3.000000)
[01:51:38 -258275.113147] FAST spr round 1 (radius: 25)
[01:53:37 -221136.041146] FAST spr round 2 (radius: 25)
[01:55:13 -219056.618381] FAST spr round 3 (radius: 25)
[01:56:42 -218947.461618] FAST spr round 4 (radius: 25)
[01:58:03 -218926.341167] FAST spr round 5 (radius: 25)
[01:59:20 -218924.903776] FAST spr round 6 (radius: 25)
[02:00:35 -218924.903773] Model parameter optimization (eps = 1.000000)
[02:00:45 -218921.521761] SLOW spr round 1 (radius: 5)
[02:02:31 -218875.388485] SLOW spr round 2 (radius: 5)
[02:04:13 -218864.348570] SLOW spr round 3 (radius: 5)
[02:05:49 -218861.742288] SLOW spr round 4 (radius: 5)
[02:07:23 -218861.742230] SLOW spr round 5 (radius: 10)
[02:09:00 -218861.742229] SLOW spr round 6 (radius: 15)
[02:11:35 -218852.897514] SLOW spr round 7 (radius: 5)
[02:13:37 -218851.778482] SLOW spr round 8 (radius: 5)
[02:15:24 -218851.778459] SLOW spr round 9 (radius: 10)
[02:17:06 -218851.778459] SLOW spr round 10 (radius: 15)
[02:19:35 -218851.778459] SLOW spr round 11 (radius: 20)
[02:23:29 -218851.778459] SLOW spr round 12 (radius: 25)
[02:28:18 -218851.778459] Model parameter optimization (eps = 0.100000)

[02:28:24] ML tree search #3, logLikelihood: -218851.572177

[02:28:24 -862276.995226] Initial branch length optimization
[02:28:27 -713519.510002] Model parameter optimization (eps = 10.000000)
[02:28:48 -712991.707096] AUTODETECT spr round 1 (radius: 5)
[02:30:22 -507378.650648] AUTODETECT spr round 2 (radius: 10)
[02:32:12 -374372.965256] AUTODETECT spr round 3 (radius: 15)
[02:34:10 -307938.581108] AUTODETECT spr round 4 (radius: 20)
[02:36:13 -270717.910124] AUTODETECT spr round 5 (radius: 25)
[02:38:26 -257775.434572] SPR radius for FAST iterations: 25 (autodetect)
[02:38:26 -257775.434572] Model parameter optimization (eps = 3.000000)
[02:38:39 -257743.582895] FAST spr round 1 (radius: 25)
[02:40:35 -220691.562199] FAST spr round 2 (radius: 25)
[02:42:08 -219033.050549] FAST spr round 3 (radius: 25)
[02:43:30 -218902.912116] FAST spr round 4 (radius: 25)
[02:44:50 -218876.805708] FAST spr round 5 (radius: 25)
[02:46:01 -218876.804792] Model parameter optimization (eps = 1.000000)
[02:46:10 -218872.622011] SLOW spr round 1 (radius: 5)
[02:47:57 -218836.947919] SLOW spr round 2 (radius: 5)
[02:49:39 -218829.421352] SLOW spr round 3 (radius: 5)
[02:51:18 -218828.089602] SLOW spr round 4 (radius: 5)
[02:52:55 -218828.089569] SLOW spr round 5 (radius: 10)
[02:54:34 -218827.737091] SLOW spr round 6 (radius: 5)
[02:56:32 -218826.178039] SLOW spr round 7 (radius: 5)
[02:58:17 -218826.178019] SLOW spr round 8 (radius: 10)
[03:00:00 -218826.086422] SLOW spr round 9 (radius: 15)
[03:02:31 -218826.085845] SLOW spr round 10 (radius: 20)
[03:05:51 -218826.085842] SLOW spr round 11 (radius: 25)
[03:09:53 -218826.085842] Model parameter optimization (eps = 0.100000)

[03:09:58] ML tree search #4, logLikelihood: -218825.765992

[03:09:58 -859152.726076] Initial branch length optimization
[03:10:00 -714566.203874] Model parameter optimization (eps = 10.000000)
[03:10:21 -714024.574695] AUTODETECT spr round 1 (radius: 5)
[03:11:43 -496901.824467] AUTODETECT spr round 2 (radius: 10)
[03:13:18 -379651.656564] AUTODETECT spr round 3 (radius: 15)
[03:15:03 -302861.800479] AUTODETECT spr round 4 (radius: 20)
[03:16:53 -269719.253859] AUTODETECT spr round 5 (radius: 25)
[03:18:53 -256758.464161] SPR radius for FAST iterations: 25 (autodetect)
[03:18:53 -256758.464161] Model parameter optimization (eps = 3.000000)
[03:19:09 -256709.438768] FAST spr round 1 (radius: 25)
[03:21:43 -220470.308052] FAST spr round 2 (radius: 25)
[03:23:24 -218992.220507] FAST spr round 3 (radius: 25)
[03:24:59 -218921.261430] FAST spr round 4 (radius: 25)
[03:26:24 -218894.364214] FAST spr round 5 (radius: 25)
[03:27:46 -218894.363912] Model parameter optimization (eps = 1.000000)
[03:27:53 -218893.529688] SLOW spr round 1 (radius: 5)
[03:29:44 -218850.327955] SLOW spr round 2 (radius: 5)
[03:31:29 -218849.276008] SLOW spr round 3 (radius: 5)
[03:33:10 -218849.275993] SLOW spr round 4 (radius: 10)
[03:34:55 -218849.067881] SLOW spr round 5 (radius: 5)
[03:36:59 -218846.634187] SLOW spr round 6 (radius: 5)
[03:38:51 -218846.634177] SLOW spr round 7 (radius: 10)
[03:40:38 -218846.634177] SLOW spr round 8 (radius: 15)
[03:43:21 -218846.235447] SLOW spr round 9 (radius: 5)
[03:45:32 -218844.220486] SLOW spr round 10 (radius: 5)
[03:47:28 -218844.220223] SLOW spr round 11 (radius: 10)
[03:49:19 -218844.220221] SLOW spr round 12 (radius: 15)
[03:51:58 -218844.220221] SLOW spr round 13 (radius: 20)
[03:56:11 -218844.220221] SLOW spr round 14 (radius: 25)
[04:01:32 -218844.220221] Model parameter optimization (eps = 0.100000)

[04:01:39] ML tree search #5, logLikelihood: -218844.040382

[04:01:39 -862321.898626] Initial branch length optimization
[04:01:41 -716234.053434] Model parameter optimization (eps = 10.000000)
[04:02:02 -715845.627293] AUTODETECT spr round 1 (radius: 5)
[04:03:47 -507261.075400] AUTODETECT spr round 2 (radius: 10)
[04:05:47 -377439.346920] AUTODETECT spr round 3 (radius: 15)
[04:07:52 -306013.977285] AUTODETECT spr round 4 (radius: 20)
[04:10:14 -266385.464209] AUTODETECT spr round 5 (radius: 25)
[04:12:38 -258336.804449] SPR radius for FAST iterations: 25 (autodetect)
[04:12:38 -258336.804449] Model parameter optimization (eps = 3.000000)
[04:12:54 -258238.886875] FAST spr round 1 (radius: 25)
[04:14:59 -220673.975275] FAST spr round 2 (radius: 25)
[04:16:43 -219084.419495] FAST spr round 3 (radius: 25)
[04:18:19 -218929.431204] FAST spr round 4 (radius: 25)
[04:19:49 -218907.012054] FAST spr round 5 (radius: 25)
[04:21:12 -218903.125569] FAST spr round 6 (radius: 25)
[04:22:33 -218903.125534] Model parameter optimization (eps = 1.000000)
[04:22:42 -218899.527082] SLOW spr round 1 (radius: 5)
[04:24:32 -218859.239917] SLOW spr round 2 (radius: 5)
[04:26:18 -218856.020581] SLOW spr round 3 (radius: 5)
[04:27:59 -218856.020467] SLOW spr round 4 (radius: 10)
[04:29:46 -218851.224644] SLOW spr round 5 (radius: 5)
[04:31:50 -218851.197560] SLOW spr round 6 (radius: 10)
[04:33:45 -218847.370280] SLOW spr round 7 (radius: 5)
[04:35:46 -218847.370113] SLOW spr round 8 (radius: 10)
[04:37:38 -218846.669122] SLOW spr round 9 (radius: 5)
[04:39:40 -218846.550220] SLOW spr round 10 (radius: 5)
[04:41:32 -218846.550184] SLOW spr round 11 (radius: 10)
[04:43:19 -218846.550184] SLOW spr round 12 (radius: 15)
[04:45:58 -218846.550184] SLOW spr round 13 (radius: 20)
[04:50:06 -218846.550184] SLOW spr round 14 (radius: 25)
[04:55:15 -218846.550184] Model parameter optimization (eps = 0.100000)

[04:55:19] ML tree search #6, logLikelihood: -218846.528994

[04:55:19 -858447.391856] Initial branch length optimization
[04:55:22 -712225.168950] Model parameter optimization (eps = 10.000000)
[04:55:53 -711701.368173] AUTODETECT spr round 1 (radius: 5)
[04:57:35 -503172.411232] AUTODETECT spr round 2 (radius: 10)
[04:59:38 -374270.581322] AUTODETECT spr round 3 (radius: 15)
[05:01:49 -318190.340696] AUTODETECT spr round 4 (radius: 20)
[05:04:37 -291482.470396] AUTODETECT spr round 5 (radius: 25)
[05:06:57 -268024.021460] SPR radius for FAST iterations: 25 (autodetect)
[05:06:57 -268024.021460] Model parameter optimization (eps = 3.000000)
[05:07:12 -267983.449956] FAST spr round 1 (radius: 25)
[05:09:20 -226830.020024] FAST spr round 2 (radius: 25)
[05:11:03 -219488.212408] FAST spr round 3 (radius: 25)
[05:12:38 -218970.212682] FAST spr round 4 (radius: 25)
[05:14:05 -218919.601542] FAST spr round 5 (radius: 25)
[05:15:27 -218916.710140] FAST spr round 6 (radius: 25)
[05:16:47 -218916.709965] Model parameter optimization (eps = 1.000000)
[05:17:01 -218914.380724] SLOW spr round 1 (radius: 5)
[05:18:55 -218851.254182] SLOW spr round 2 (radius: 5)
[05:20:41 -218845.328954] SLOW spr round 3 (radius: 5)
[05:22:22 -218845.328878] SLOW spr round 4 (radius: 10)
[05:24:07 -218842.768851] SLOW spr round 5 (radius: 5)
[05:26:11 -218841.528030] SLOW spr round 6 (radius: 5)
[05:28:05 -218841.353380] SLOW spr round 7 (radius: 5)
[05:29:51 -218841.353178] SLOW spr round 8 (radius: 10)
[05:31:36 -218841.353177] SLOW spr round 9 (radius: 15)
[05:34:24 -218841.353177] SLOW spr round 10 (radius: 20)
[05:38:42 -218841.353177] SLOW spr round 11 (radius: 25)
[05:44:04 -218841.353177] Model parameter optimization (eps = 0.100000)

[05:44:15] ML tree search #7, logLikelihood: -218840.726558

[05:44:15 -856918.685395] Initial branch length optimization
[05:44:17 -711222.862881] Model parameter optimization (eps = 10.000000)
[05:44:43 -710751.294183] AUTODETECT spr round 1 (radius: 5)
[05:46:26 -485837.705188] AUTODETECT spr round 2 (radius: 10)
[05:48:24 -358125.204995] AUTODETECT spr round 3 (radius: 15)
[05:50:34 -300010.701955] AUTODETECT spr round 4 (radius: 20)
[05:52:50 -263080.315795] AUTODETECT spr round 5 (radius: 25)
[05:55:30 -254453.295546] SPR radius for FAST iterations: 25 (autodetect)
[05:55:30 -254453.295546] Model parameter optimization (eps = 3.000000)
[05:55:45 -254396.071163] FAST spr round 1 (radius: 25)
[05:57:54 -220686.833552] FAST spr round 2 (radius: 25)
[05:59:35 -219178.236376] FAST spr round 3 (radius: 25)
[06:01:14 -218945.652711] FAST spr round 4 (radius: 25)
[06:02:41 -218912.399268] FAST spr round 5 (radius: 25)
[06:04:03 -218910.410301] FAST spr round 6 (radius: 25)
[06:05:23 -218910.410204] Model parameter optimization (eps = 1.000000)
[06:05:36 -218902.395733] SLOW spr round 1 (radius: 5)
[06:07:27 -218857.774836] SLOW spr round 2 (radius: 5)
[06:09:17 -218848.215124] SLOW spr round 3 (radius: 5)
[06:11:02 -218845.638692] SLOW spr round 4 (radius: 5)
[06:12:44 -218845.638492] SLOW spr round 5 (radius: 10)
[06:14:29 -218840.347531] SLOW spr round 6 (radius: 5)
[06:16:33 -218840.347431] SLOW spr round 7 (radius: 10)
[06:18:29 -218840.347431] SLOW spr round 8 (radius: 15)
[06:21:08 -218840.347431] SLOW spr round 9 (radius: 20)
[06:25:33 -218840.347431] SLOW spr round 10 (radius: 25)
[06:30:54 -218840.347431] Model parameter optimization (eps = 0.100000)

[06:31:04] ML tree search #8, logLikelihood: -218840.184257

[06:31:04 -869282.681796] Initial branch length optimization
[06:31:06 -717381.843290] Model parameter optimization (eps = 10.000000)
[06:31:30 -716860.155442] AUTODETECT spr round 1 (radius: 5)
[06:33:13 -501123.276063] AUTODETECT spr round 2 (radius: 10)
[06:35:05 -372508.476465] AUTODETECT spr round 3 (radius: 15)
[06:37:13 -302562.131973] AUTODETECT spr round 4 (radius: 20)
[06:39:29 -270510.106779] AUTODETECT spr round 5 (radius: 25)
[06:42:29 -256013.009840] SPR radius for FAST iterations: 25 (autodetect)
[06:42:29 -256013.009840] Model parameter optimization (eps = 3.000000)
[06:42:43 -255963.737099] FAST spr round 1 (radius: 25)
[06:44:47 -220255.042291] FAST spr round 2 (radius: 25)
[06:46:24 -218938.852215] FAST spr round 3 (radius: 25)
[06:47:54 -218905.139722] FAST spr round 4 (radius: 25)
[06:49:16 -218901.033557] FAST spr round 5 (radius: 25)
[06:50:37 -218901.033295] Model parameter optimization (eps = 1.000000)
[06:50:53 -218894.303645] SLOW spr round 1 (radius: 5)
[06:52:47 -218853.485199] SLOW spr round 2 (radius: 5)
[06:54:33 -218846.215810] SLOW spr round 3 (radius: 5)
[06:56:13 -218846.215612] SLOW spr round 4 (radius: 10)
[06:57:58 -218844.773152] SLOW spr round 5 (radius: 5)
[07:00:01 -218844.773151] SLOW spr round 6 (radius: 10)
[07:01:57 -218844.579879] SLOW spr round 7 (radius: 5)
[07:04:03 -218834.754887] SLOW spr round 8 (radius: 5)
[07:05:55 -218831.322556] SLOW spr round 9 (radius: 5)
[07:07:39 -218831.322533] SLOW spr round 10 (radius: 10)
[07:09:24 -218831.283141] SLOW spr round 11 (radius: 15)
[07:12:08 -218831.281927] SLOW spr round 12 (radius: 20)
[07:16:17 -218831.281922] SLOW spr round 13 (radius: 25)
[07:21:25 -218831.281922] Model parameter optimization (eps = 0.100000)

[07:21:32] ML tree search #9, logLikelihood: -218831.150587

[07:21:32 -862928.101845] Initial branch length optimization
[07:21:35 -713604.208317] Model parameter optimization (eps = 10.000000)
[07:22:08 -713074.495064] AUTODETECT spr round 1 (radius: 5)
[07:23:52 -503867.762212] AUTODETECT spr round 2 (radius: 10)
[07:25:52 -387532.935683] AUTODETECT spr round 3 (radius: 15)
[07:28:02 -330012.781306] AUTODETECT spr round 4 (radius: 20)
[07:30:46 -284572.798068] AUTODETECT spr round 5 (radius: 25)
[07:33:07 -272023.337073] SPR radius for FAST iterations: 25 (autodetect)
[07:33:07 -272023.337073] Model parameter optimization (eps = 3.000000)
[07:33:22 -271920.739193] FAST spr round 1 (radius: 25)
[07:35:27 -220910.903473] FAST spr round 2 (radius: 25)
[07:37:10 -219048.361394] FAST spr round 3 (radius: 25)
[07:38:42 -218923.366748] FAST spr round 4 (radius: 25)
[07:40:07 -218910.473950] FAST spr round 5 (radius: 25)
[07:41:29 -218908.994921] FAST spr round 6 (radius: 25)
[07:42:49 -218908.994578] Model parameter optimization (eps = 1.000000)
[07:42:56 -218908.378862] SLOW spr round 1 (radius: 5)
[07:44:47 -218873.680042] SLOW spr round 2 (radius: 5)
[07:46:33 -218870.901517] SLOW spr round 3 (radius: 5)
[07:48:16 -218870.901480] SLOW spr round 4 (radius: 10)
[07:50:02 -218867.252405] SLOW spr round 5 (radius: 5)
[07:52:08 -218866.405903] SLOW spr round 6 (radius: 5)
[07:53:59 -218866.405880] SLOW spr round 7 (radius: 10)
[07:55:50 -218866.405880] SLOW spr round 8 (radius: 15)
[07:58:27 -218859.431125] SLOW spr round 9 (radius: 5)
[08:00:38 -218858.907849] SLOW spr round 10 (radius: 5)
[08:02:35 -218858.727117] SLOW spr round 11 (radius: 5)
[08:04:22 -218858.726689] SLOW spr round 12 (radius: 10)
[08:06:11 -218858.726686] SLOW spr round 13 (radius: 15)
[08:08:51 -218858.726686] SLOW spr round 14 (radius: 20)
[08:12:43 -218858.726686] SLOW spr round 15 (radius: 25)
[08:17:25 -218858.726686] Model parameter optimization (eps = 0.100000)

[08:17:32] ML tree search #10, logLikelihood: -218858.605047

[08:17:32 -863292.690276] Initial branch length optimization
[08:17:35 -713873.861159] Model parameter optimization (eps = 10.000000)
[08:18:00 -713286.048420] AUTODETECT spr round 1 (radius: 5)
[08:19:44 -503769.317993] AUTODETECT spr round 2 (radius: 10)
[08:21:46 -372632.573164] AUTODETECT spr round 3 (radius: 15)
[08:24:00 -304091.707127] AUTODETECT spr round 4 (radius: 20)
[08:26:27 -274906.444883] AUTODETECT spr round 5 (radius: 25)
[08:29:00 -258455.742218] SPR radius for FAST iterations: 25 (autodetect)
[08:29:00 -258455.742218] Model parameter optimization (eps = 3.000000)
[08:29:17 -258397.229353] FAST spr round 1 (radius: 25)
[08:31:27 -220507.288506] FAST spr round 2 (radius: 25)
[08:33:10 -218988.583374] FAST spr round 3 (radius: 25)
[08:34:44 -218934.489164] FAST spr round 4 (radius: 25)
[08:36:07 -218927.290221] FAST spr round 5 (radius: 25)
[08:37:29 -218916.513528] FAST spr round 6 (radius: 25)
[08:38:50 -218911.244261] FAST spr round 7 (radius: 25)
[08:40:10 -218911.244258] Model parameter optimization (eps = 1.000000)
[08:40:15 -218910.752448] SLOW spr round 1 (radius: 5)
[08:42:05 -218849.965828] SLOW spr round 2 (radius: 5)
[08:43:50 -218847.167224] SLOW spr round 3 (radius: 5)
[08:45:32 -218846.304653] SLOW spr round 4 (radius: 5)
[08:47:12 -218845.436188] SLOW spr round 5 (radius: 5)
[08:48:54 -218844.645729] SLOW spr round 6 (radius: 5)
[08:50:33 -218844.645708] SLOW spr round 7 (radius: 10)
[08:52:17 -218842.155605] SLOW spr round 8 (radius: 5)
[08:54:21 -218842.155458] SLOW spr round 9 (radius: 10)
[08:56:12 -218842.155457] SLOW spr round 10 (radius: 15)
[08:58:48 -218842.155457] SLOW spr round 11 (radius: 20)
[09:03:06 -218842.155457] SLOW spr round 12 (radius: 25)
[09:08:16 -218842.155457] Model parameter optimization (eps = 0.100000)

[09:08:23] ML tree search #11, logLikelihood: -218842.029461

[09:08:23 -862157.469998] Initial branch length optimization
[09:08:26 -714184.104941] Model parameter optimization (eps = 10.000000)
[09:08:48 -713692.514879] AUTODETECT spr round 1 (radius: 5)
[09:10:31 -500101.354181] AUTODETECT spr round 2 (radius: 10)
[09:12:30 -377483.118983] AUTODETECT spr round 3 (radius: 15)
[09:14:37 -297315.843306] AUTODETECT spr round 4 (radius: 20)
[09:16:50 -270594.616839] AUTODETECT spr round 5 (radius: 25)
[09:19:06 -256831.174248] SPR radius for FAST iterations: 25 (autodetect)
[09:19:06 -256831.174248] Model parameter optimization (eps = 3.000000)
[09:19:22 -256780.607246] FAST spr round 1 (radius: 25)
[09:21:27 -223432.166700] FAST spr round 2 (radius: 25)
[09:23:07 -219126.592308] FAST spr round 3 (radius: 25)
[09:24:38 -218948.192189] FAST spr round 4 (radius: 25)
[09:26:06 -218918.923068] FAST spr round 5 (radius: 25)
[09:27:27 -218918.923049] Model parameter optimization (eps = 1.000000)
[09:27:38 -218917.490094] SLOW spr round 1 (radius: 5)
[09:29:28 -218863.725743] SLOW spr round 2 (radius: 5)
[09:31:06 -218861.256887] SLOW spr round 3 (radius: 5)
[09:32:47 -218860.838587] SLOW spr round 4 (radius: 5)
[09:34:28 -218860.838230] SLOW spr round 5 (radius: 10)
[09:36:14 -218856.957530] SLOW spr round 6 (radius: 5)
[09:38:21 -218846.629427] SLOW spr round 7 (radius: 5)
[09:40:13 -218845.251705] SLOW spr round 8 (radius: 5)
[09:41:59 -218845.251701] SLOW spr round 9 (radius: 10)
[09:43:45 -218844.706448] SLOW spr round 10 (radius: 5)
[09:45:48 -218844.585453] SLOW spr round 11 (radius: 5)
[09:47:40 -218844.585400] SLOW spr round 12 (radius: 10)
[09:49:30 -218844.585400] SLOW spr round 13 (radius: 15)
[09:52:13 -218844.585400] SLOW spr round 14 (radius: 20)
[09:56:26 -218844.585400] SLOW spr round 15 (radius: 25)
[10:01:37 -218844.585400] Model parameter optimization (eps = 0.100000)

[10:01:41] ML tree search #12, logLikelihood: -218844.557162

[10:01:41 -859166.077462] Initial branch length optimization
[10:01:44 -712012.599512] Model parameter optimization (eps = 10.000000)
[10:02:12 -711487.120792] AUTODETECT spr round 1 (radius: 5)
[10:03:55 -499763.107715] AUTODETECT spr round 2 (radius: 10)
[10:05:53 -378528.334814] AUTODETECT spr round 3 (radius: 15)
[10:08:09 -293960.988711] AUTODETECT spr round 4 (radius: 20)
[10:10:22 -267512.354534] AUTODETECT spr round 5 (radius: 25)
[10:12:51 -259130.788426] SPR radius for FAST iterations: 25 (autodetect)
[10:12:51 -259130.788426] Model parameter optimization (eps = 3.000000)
[10:13:04 -259043.290941] FAST spr round 1 (radius: 25)
[10:14:40 -225478.585886] FAST spr round 2 (radius: 25)
[10:16:01 -219644.321348] FAST spr round 3 (radius: 25)
[10:17:16 -218923.578582] FAST spr round 4 (radius: 25)
[10:18:26 -218908.735663] FAST spr round 5 (radius: 25)
[10:19:49 -218907.432686] FAST spr round 6 (radius: 25)
[10:21:08 -218907.432675] Model parameter optimization (eps = 1.000000)
[10:21:20 -218904.009920] SLOW spr round 1 (radius: 5)
[10:23:12 -218842.830596] SLOW spr round 2 (radius: 5)
[10:25:00 -218834.753739] SLOW spr round 3 (radius: 5)
[10:26:43 -218833.854673] SLOW spr round 4 (radius: 5)
[10:28:26 -218831.673587] SLOW spr round 5 (radius: 5)
[10:30:07 -218831.673511] SLOW spr round 6 (radius: 10)
[10:31:53 -218831.673511] SLOW spr round 7 (radius: 15)
[10:34:40 -218831.472428] SLOW spr round 8 (radius: 5)
[10:36:52 -218831.267553] SLOW spr round 9 (radius: 5)
[10:38:49 -218831.267503] SLOW spr round 10 (radius: 10)
[10:40:39 -218831.267500] SLOW spr round 11 (radius: 15)
[10:43:20 -218831.267500] SLOW spr round 12 (radius: 20)
[10:47:33 -218831.267500] SLOW spr round 13 (radius: 25)
[10:52:43 -218831.267500] Model parameter optimization (eps = 0.100000)

[10:52:50] ML tree search #13, logLikelihood: -218831.116241

[10:52:50 -858472.599646] Initial branch length optimization
[10:52:54 -713971.458715] Model parameter optimization (eps = 10.000000)
[10:53:21 -713574.524034] AUTODETECT spr round 1 (radius: 5)
[10:55:05 -498093.745011] AUTODETECT spr round 2 (radius: 10)
[10:57:07 -360927.664209] AUTODETECT spr round 3 (radius: 15)
[10:59:24 -300310.970155] AUTODETECT spr round 4 (radius: 20)
[11:01:57 -264999.191923] AUTODETECT spr round 5 (radius: 25)
[11:04:19 -252869.762711] SPR radius for FAST iterations: 25 (autodetect)
[11:04:19 -252869.762711] Model parameter optimization (eps = 3.000000)
[11:04:36 -252778.423085] FAST spr round 1 (radius: 25)
[11:06:42 -219924.693120] FAST spr round 2 (radius: 25)
[11:08:25 -218998.388266] FAST spr round 3 (radius: 25)
[11:10:00 -218941.307545] FAST spr round 4 (radius: 25)
[11:11:28 -218928.535804] FAST spr round 5 (radius: 25)
[11:12:50 -218924.748481] FAST spr round 6 (radius: 25)
[11:14:09 -218924.746263] Model parameter optimization (eps = 1.000000)
[11:14:19 -218923.746538] SLOW spr round 1 (radius: 5)
[11:16:14 -218868.354681] SLOW spr round 2 (radius: 5)
[11:18:01 -218865.524882] SLOW spr round 3 (radius: 5)
[11:19:44 -218865.451280] SLOW spr round 4 (radius: 10)
[11:21:31 -218864.280867] SLOW spr round 5 (radius: 5)
[11:23:38 -218861.614273] SLOW spr round 6 (radius: 5)
[11:25:30 -218861.614106] SLOW spr round 7 (radius: 10)
[11:27:19 -218861.614105] SLOW spr round 8 (radius: 15)
[11:30:01 -218861.614105] SLOW spr round 9 (radius: 20)
[11:34:12 -218861.614105] SLOW spr round 10 (radius: 25)
[11:39:19 -218861.614105] Model parameter optimization (eps = 0.100000)

[11:39:26] ML tree search #14, logLikelihood: -218861.406878

[11:39:26 -861656.500954] Initial branch length optimization
[11:39:29 -712674.761723] Model parameter optimization (eps = 10.000000)
[11:39:52 -712214.589941] AUTODETECT spr round 1 (radius: 5)
[11:41:37 -499517.579703] AUTODETECT spr round 2 (radius: 10)
[11:43:35 -371720.451533] AUTODETECT spr round 3 (radius: 15)
[11:45:47 -309113.234199] AUTODETECT spr round 4 (radius: 20)
[11:48:10 -287144.733698] AUTODETECT spr round 5 (radius: 25)
[11:50:56 -265314.387506] SPR radius for FAST iterations: 25 (autodetect)
[11:50:56 -265314.387506] Model parameter optimization (eps = 3.000000)
[11:51:13 -265237.649398] FAST spr round 1 (radius: 25)
[11:53:25 -221526.256911] FAST spr round 2 (radius: 25)
[11:55:10 -219198.011708] FAST spr round 3 (radius: 25)
[11:56:45 -218936.758241] FAST spr round 4 (radius: 25)
[11:58:13 -218912.553147] FAST spr round 5 (radius: 25)
[11:59:35 -218909.999989] FAST spr round 6 (radius: 25)
[12:00:55 -218909.999934] Model parameter optimization (eps = 1.000000)
[12:01:08 -218908.183527] SLOW spr round 1 (radius: 5)
[12:03:00 -218860.060652] SLOW spr round 2 (radius: 5)
[12:04:45 -218857.444860] SLOW spr round 3 (radius: 5)
[12:06:27 -218857.444748] SLOW spr round 4 (radius: 10)
[12:08:13 -218856.532820] SLOW spr round 5 (radius: 5)
[12:10:21 -218853.143455] SLOW spr round 6 (radius: 5)
[12:12:14 -218853.143409] SLOW spr round 7 (radius: 10)
[12:14:02 -218853.143408] SLOW spr round 8 (radius: 15)
[12:16:44 -218853.143408] SLOW spr round 9 (radius: 20)
[12:20:55 -218853.143408] SLOW spr round 10 (radius: 25)
[12:26:04 -218853.143408] Model parameter optimization (eps = 0.100000)

[12:26:08] ML tree search #15, logLikelihood: -218853.115266

[12:26:08 -852910.144372] Initial branch length optimization
[12:26:10 -706619.060080] Model parameter optimization (eps = 10.000000)
[12:26:33 -706235.237823] AUTODETECT spr round 1 (radius: 5)
[12:28:16 -498784.425306] AUTODETECT spr round 2 (radius: 10)
[12:30:14 -374401.783982] AUTODETECT spr round 3 (radius: 15)
[12:32:24 -315219.359550] AUTODETECT spr round 4 (radius: 20)
[12:35:08 -285315.124564] AUTODETECT spr round 5 (radius: 25)
[12:38:02 -259923.809825] SPR radius for FAST iterations: 25 (autodetect)
[12:38:02 -259923.809825] Model parameter optimization (eps = 3.000000)
[12:38:09 -259918.724003] FAST spr round 1 (radius: 25)
[12:40:09 -220848.710639] FAST spr round 2 (radius: 25)
[12:41:50 -219108.592137] FAST spr round 3 (radius: 25)
[12:43:21 -219016.713305] FAST spr round 4 (radius: 25)
[12:44:47 -219000.904988] FAST spr round 5 (radius: 25)
[12:46:09 -218998.339220] FAST spr round 6 (radius: 25)
[12:47:28 -218998.338736] Model parameter optimization (eps = 1.000000)
[12:47:44 -218930.352905] SLOW spr round 1 (radius: 5)
[12:49:36 -218869.272277] SLOW spr round 2 (radius: 5)
[12:51:22 -218858.686154] SLOW spr round 3 (radius: 5)
[12:53:06 -218857.598179] SLOW spr round 4 (radius: 5)
[12:54:48 -218857.598027] SLOW spr round 5 (radius: 10)
[12:56:34 -218854.908771] SLOW spr round 6 (radius: 5)
[12:58:41 -218846.779775] SLOW spr round 7 (radius: 5)
[13:00:34 -218845.544885] SLOW spr round 8 (radius: 5)
[13:02:21 -218844.902694] SLOW spr round 9 (radius: 5)
[13:04:05 -218844.902645] SLOW spr round 10 (radius: 10)
[13:05:49 -218844.902644] SLOW spr round 11 (radius: 15)
[13:08:35 -218844.902644] SLOW spr round 12 (radius: 20)
[13:12:50 -218844.902644] SLOW spr round 13 (radius: 25)
[13:18:15 -218844.902644] Model parameter optimization (eps = 0.100000)

[13:18:24] ML tree search #16, logLikelihood: -218844.313557

[13:18:24 -863381.996794] Initial branch length optimization
[13:18:27 -718104.405363] Model parameter optimization (eps = 10.000000)
[13:18:50 -717587.438121] AUTODETECT spr round 1 (radius: 5)
[13:20:35 -501830.618169] AUTODETECT spr round 2 (radius: 10)
[13:22:34 -391630.188816] AUTODETECT spr round 3 (radius: 15)
[13:24:53 -317418.941959] AUTODETECT spr round 4 (radius: 20)
[13:27:20 -289729.446041] AUTODETECT spr round 5 (radius: 25)
[13:29:50 -261065.722698] SPR radius for FAST iterations: 25 (autodetect)
[13:29:50 -261065.722698] Model parameter optimization (eps = 3.000000)
[13:30:05 -261016.585288] FAST spr round 1 (radius: 25)
[13:32:10 -221467.898293] FAST spr round 2 (radius: 25)
[13:33:49 -219255.660798] FAST spr round 3 (radius: 25)
[13:35:22 -218969.340227] FAST spr round 4 (radius: 25)
[13:36:50 -218941.023771] FAST spr round 5 (radius: 25)
[13:38:12 -218937.252187] FAST spr round 6 (radius: 25)
[13:39:32 -218937.252148] Model parameter optimization (eps = 1.000000)
[13:39:44 -218934.730088] SLOW spr round 1 (radius: 5)
[13:41:35 -218864.881049] SLOW spr round 2 (radius: 5)
[13:43:23 -218853.286441] SLOW spr round 3 (radius: 5)
[13:45:09 -218849.444519] SLOW spr round 4 (radius: 5)
[13:46:51 -218849.442377] SLOW spr round 5 (radius: 10)
[13:48:36 -218849.442337] SLOW spr round 6 (radius: 15)
[13:51:21 -218849.442337] SLOW spr round 7 (radius: 20)
[13:55:37 -218849.442337] SLOW spr round 8 (radius: 25)
[14:00:55 -218849.442337] Model parameter optimization (eps = 0.100000)

[14:01:02] ML tree search #17, logLikelihood: -218849.296580

[14:01:02 -864926.485870] Initial branch length optimization
[14:01:06 -716446.702393] Model parameter optimization (eps = 10.000000)
[14:01:25 -715898.201513] AUTODETECT spr round 1 (radius: 5)
[14:03:07 -501989.982612] AUTODETECT spr round 2 (radius: 10)
[14:05:06 -380519.442768] AUTODETECT spr round 3 (radius: 15)
[14:07:24 -310633.435631] AUTODETECT spr round 4 (radius: 20)
[14:09:52 -279125.357634] AUTODETECT spr round 5 (radius: 25)
[14:12:53 -262939.769228] SPR radius for FAST iterations: 25 (autodetect)
[14:12:53 -262939.769228] Model parameter optimization (eps = 3.000000)
[14:13:00 -262936.417467] FAST spr round 1 (radius: 25)
[14:15:08 -221114.377118] FAST spr round 2 (radius: 25)
[14:16:50 -219136.345282] FAST spr round 3 (radius: 25)
[14:18:23 -218973.554386] FAST spr round 4 (radius: 25)
[14:19:51 -218953.869940] FAST spr round 5 (radius: 25)
[14:21:13 -218947.961368] FAST spr round 6 (radius: 25)
[14:22:34 -218947.389879] FAST spr round 7 (radius: 25)
[14:23:54 -218947.388991] Model parameter optimization (eps = 1.000000)
[14:24:08 -218912.044427] SLOW spr round 1 (radius: 5)
[14:25:57 -218857.599112] SLOW spr round 2 (radius: 5)
[14:27:20 -218852.438577] SLOW spr round 3 (radius: 5)
[14:28:41 -218852.438092] SLOW spr round 4 (radius: 10)
[14:30:04 -218852.438087] SLOW spr round 5 (radius: 15)
[14:32:16 -218846.577874] SLOW spr round 6 (radius: 5)
[14:33:59 -218845.986147] SLOW spr round 7 (radius: 5)
[14:35:30 -218845.986105] SLOW spr round 8 (radius: 10)
[14:36:56 -218845.986104] SLOW spr round 9 (radius: 15)
[14:39:03 -218845.986104] SLOW spr round 10 (radius: 20)
[14:42:21 -218845.986104] SLOW spr round 11 (radius: 25)
[14:46:21 -218845.986104] Model parameter optimization (eps = 0.100000)

[14:46:27] ML tree search #18, logLikelihood: -218845.634470

[14:46:27 -870678.739818] Initial branch length optimization
[14:46:30 -720289.045214] Model parameter optimization (eps = 10.000000)
[14:46:49 -719794.086769] AUTODETECT spr round 1 (radius: 5)
[14:48:12 -497619.931768] AUTODETECT spr round 2 (radius: 10)
[14:49:46 -381529.757707] AUTODETECT spr round 3 (radius: 15)
[14:51:27 -324876.115197] AUTODETECT spr round 4 (radius: 20)
[14:53:34 -271785.525193] AUTODETECT spr round 5 (radius: 25)
[14:55:20 -263533.185146] SPR radius for FAST iterations: 25 (autodetect)
[14:55:20 -263533.185146] Model parameter optimization (eps = 3.000000)
[14:55:33 -263471.744391] FAST spr round 1 (radius: 25)
[14:57:15 -222814.493741] FAST spr round 2 (radius: 25)
[14:58:39 -219077.948364] FAST spr round 3 (radius: 25)
[14:59:54 -218966.574790] FAST spr round 4 (radius: 25)
[15:01:02 -218946.771801] FAST spr round 5 (radius: 25)
[15:02:07 -218943.660331] FAST spr round 6 (radius: 25)
[15:03:10 -218943.660307] Model parameter optimization (eps = 1.000000)
[15:03:15 -218943.269905] SLOW spr round 1 (radius: 5)
[15:04:45 -218880.918033] SLOW spr round 2 (radius: 5)
[15:06:26 -218871.037757] SLOW spr round 3 (radius: 5)
[15:08:06 -218871.037740] SLOW spr round 4 (radius: 10)
[15:09:52 -218863.854587] SLOW spr round 5 (radius: 5)
[15:11:56 -218863.084354] SLOW spr round 6 (radius: 5)
[15:13:47 -218863.082805] SLOW spr round 7 (radius: 10)
[15:15:35 -218863.082701] SLOW spr round 8 (radius: 15)
[15:18:17 -218863.082693] SLOW spr round 9 (radius: 20)
[15:22:28 -218863.082693] SLOW spr round 10 (radius: 25)
[15:27:37 -218863.082693] Model parameter optimization (eps = 0.100000)

[15:27:44] ML tree search #19, logLikelihood: -218863.018896

[15:27:44 -856953.813031] Initial branch length optimization
[15:27:47 -711383.256407] Model parameter optimization (eps = 10.000000)
[15:28:10 -710664.721085] AUTODETECT spr round 1 (radius: 5)
[15:29:53 -500125.702391] AUTODETECT spr round 2 (radius: 10)
[15:31:50 -358491.151290] AUTODETECT spr round 3 (radius: 15)
[15:34:01 -292696.521207] AUTODETECT spr round 4 (radius: 20)
[15:36:21 -256844.641150] AUTODETECT spr round 5 (radius: 25)
[15:38:46 -250786.080719] SPR radius for FAST iterations: 25 (autodetect)
[15:38:46 -250786.080719] Model parameter optimization (eps = 3.000000)
[15:39:03 -250727.942606] FAST spr round 1 (radius: 25)
[15:41:06 -219889.570694] FAST spr round 2 (radius: 25)
[15:42:40 -218965.418819] FAST spr round 3 (radius: 25)
[15:44:09 -218906.158550] FAST spr round 4 (radius: 25)
[15:45:33 -218900.485060] FAST spr round 5 (radius: 25)
[15:46:53 -218900.483418] Model parameter optimization (eps = 1.000000)
[15:47:05 -218899.385905] SLOW spr round 1 (radius: 5)
[15:48:57 -218854.921820] SLOW spr round 2 (radius: 5)
[15:50:43 -218838.130572] SLOW spr round 3 (radius: 5)
[15:52:25 -218837.561132] SLOW spr round 4 (radius: 5)
[15:54:06 -218837.560608] SLOW spr round 5 (radius: 10)
[15:55:52 -218837.560601] SLOW spr round 6 (radius: 15)
[15:58:38 -218837.560601] SLOW spr round 7 (radius: 20)
[16:02:51 -218837.560601] SLOW spr round 8 (radius: 25)
[16:08:06 -218837.560601] Model parameter optimization (eps = 0.100000)

[16:08:12] ML tree search #20, logLikelihood: -218837.485396


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.171250,0.159783) (0.206128,0.303901) (0.296064,0.919975) (0.326559,1.952555) 
   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: -218825.765992

AIC score: 441661.531984 / AICc score: 8485721.531984 / BIC score: 449962.000511
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=464).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 57 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14807/3_mltree/Q14807.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14807/3_mltree/Q14807.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14807/3_mltree/Q14807.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14807/3_mltree/Q14807.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14807/3_mltree/Q14807.raxml.log

Analysis started: 03-Jul-2021 13:05:14 / finished: 04-Jul-2021 05:13:26

Elapsed time: 58092.394 seconds

Consumed energy: 5336.462 Wh (= 27 km in an electric car, or 133 km with an e-scooter!)