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 07-Jul-2021 05:24:29 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q15029/2_msa/Q15029_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q15029/3_mltree/Q15029 --seed 2 --threads 8 --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 (8 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q15029/2_msa/Q15029_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 1675 sites

WARNING: Sequences tr_J3KKZ6_J3KKZ6_COCIM_246410 and tr_A0A0J6YRC0_A0A0J6YRC0_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B2WDA0_B2WDA0_PYRTR_426418 and tr_A0A2W1GG03_A0A2W1GG03_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_G3RAS9_G3RAS9_GORGO_9595 and sp_Q5R8Z3_EF2_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3RAS9_G3RAS9_GORGO_9595 and tr_H2QF02_H2QF02_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RAS9_G3RAS9_GORGO_9595 and sp_P13639_EF2_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3RB35_G3RB35_GORGO_9595 and tr_G7NIZ0_G7NIZ0_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G3RB35_G3RB35_GORGO_9595 and tr_F7I888_F7I888_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G3RB35_G3RB35_GORGO_9595 and tr_G7PV09_G7PV09_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G3RB35_G3RB35_GORGO_9595 and tr_A0A096P641_A0A096P641_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G3RB35_G3RB35_GORGO_9595 and tr_A0A0D9S0P9_A0A0D9S0P9_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G3RB35_G3RB35_GORGO_9595 and tr_A0A2K5MHD2_A0A2K5MHD2_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G3RB35_G3RB35_GORGO_9595 and tr_A0A2K6CZ11_A0A2K6CZ11_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G3RB35_G3RB35_GORGO_9595 and tr_A0A2K5YPR1_A0A2K5YPR1_MANLE_9568 are exactly identical!
WARNING: Sequences tr_C0NSN4_C0NSN4_AJECG_447093 and tr_F0UUQ1_F0UUQ1_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_Q29AG5_Q29AG5_DROPS_46245 and tr_B4G6B5_B4G6B5_DROPE_7234 are exactly identical!
WARNING: Sequences tr_A0A179UAW4_A0A179UAW4_BLAGS_559298 and tr_C5GIT6_C5GIT6_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_F1PUB9_F1PUB9_CANLF_9615 and tr_F6VUI6_F6VUI6_HORSE_9796 are exactly identical!
WARNING: Sequences tr_F1PUB9_F1PUB9_CANLF_9615 and tr_G1MJ97_G1MJ97_AILME_9646 are exactly identical!
WARNING: Sequences tr_F1PUB9_F1PUB9_CANLF_9615 and tr_A0A2U3ZMP1_A0A2U3ZMP1_ODORO_9708 are exactly identical!
WARNING: Sequences tr_F1PUB9_F1PUB9_CANLF_9615 and tr_A0A384CBJ7_A0A384CBJ7_URSMA_29073 are exactly identical!
WARNING: Sequences tr_H2QD78_H2QD78_PANTR_9598 and sp_Q15029_U5S1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2QD78_H2QD78_PANTR_9598 and tr_A0A2R9AB34_A0A2R9AB34_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9FJY7_F9FJY7_FUSOF_660025 and tr_X0C0C4_X0C0C4_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FJY7_F9FJY7_FUSOF_660025 and tr_A0A2H3TJ09_A0A2H3TJ09_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_C6HG01_C6HG01_AJECH_544712 and tr_F0UMQ7_F0UMQ7_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_A0A088A5X7_A0A088A5X7_APIME_7460 and tr_A0A2A3EIV9_A0A2A3EIV9_APICC_94128 are exactly identical!
WARNING: Sequences tr_A0A088AA44_A0A088AA44_APIME_7460 and tr_A0A2A3EHA7_A0A2A3EHA7_APICC_94128 are exactly identical!
WARNING: Sequences tr_Q2TZ24_Q2TZ24_ASPOR_510516 and tr_A0A1S9DG91_A0A1S9DG91_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_C0J9X8_C0J9X8_ORYNI_4536 and tr_I1Q3J1_I1Q3J1_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_C0J9X8_C0J9X8_ORYNI_4536 and tr_A0A0E0PZZ8_A0A0E0PZZ8_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_C0J9X8_C0J9X8_ORYNI_4536 and tr_A0A0E0ABQ1_A0A0E0ABQ1_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_C0J9X8_C0J9X8_ORYNI_4536 and tr_Q69V60_Q69V60_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_G7XQX5_G7XQX5_ASPKW_1033177 and tr_A0A146FTP4_A0A146FTP4_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_F9XC91_F9XC91_ZYMTI_336722 and tr_A0A1X7RTR2_A0A1X7RTR2_ZYMTR_1276538 are exactly identical!
WARNING: Sequences tr_G2XUB4_G2XUB4_BOTF4_999810 and tr_M7U5I1_M7U5I1_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_E3NGZ9_E3NGZ9_CAERE_31234 and tr_A0A261BFB5_A0A261BFB5_9PELO_1503980 are exactly identical!
WARNING: Sequences tr_W2R8P0_W2R8P0_PHYPN_761204 and tr_A0A0W8DU86_A0A0W8DU86_PHYNI_4790 are exactly identical!
WARNING: Sequences tr_W2R8P0_W2R8P0_PHYPN_761204 and tr_W2NCI4_W2NCI4_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A0A0MUJ5_A0A0A0MUJ5_PAPAN_9555 and tr_A0A0D9REP7_A0A0D9REP7_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A0A0MUJ5_A0A0A0MUJ5_PAPAN_9555 and tr_A0A2K5N9M0_A0A2K5N9M0_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A0A0MUJ5_A0A0A0MUJ5_PAPAN_9555 and tr_A0A2K5YFX0_A0A2K5YFX0_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A151MWJ6_A0A151MWJ6_ALLMI_8496 and tr_A0A1U7S555_A0A1U7S555_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A091J4Y2_A0A091J4Y2_EGRGA_188379 and tr_A0A091VNL6_A0A091VNL6_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091J4Y2_A0A091J4Y2_EGRGA_188379 and tr_A0A087RIK5_A0A087RIK5_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091VNA1_A0A091VNA1_OPIHO_30419 and tr_A0A0A0ACG3_A0A0A0ACG3_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A0V1D7W6_A0A0V1D7W6_TRIBR_45882 and tr_A0A0V0VFA2_A0A0V0VFA2_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1D7W6_A0A0V1D7W6_TRIBR_45882 and tr_A0A0V1NQH1_A0A0V1NQH1_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V1D7W6_A0A0V1D7W6_TRIBR_45882 and tr_A0A0V0TWV0_A0A0V0TWV0_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A0V1DDM1_A0A0V1DDM1_TRIBR_45882 and tr_A0A0V0X7P5_A0A0V0X7P5_9BILA_92179 are exactly identical!
WARNING: Sequences tr_A0A0V1DDM1_A0A0V1DDM1_TRIBR_45882 and tr_A0A0V1L546_A0A0V1L546_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V0XA33_A0A0V0XA33_9BILA_92179 and tr_A0A0V1L2R7_A0A0V1L2R7_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A1S4AQA0_A0A1S4AQA0_TOBAC_4097 and tr_A0A1U7Y0V7_A0A1U7Y0V7_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A2Y9MIJ0_A0A2Y9MIJ0_DELLE_9749 and tr_A0A2Y9FKA0_A0A2Y9FKA0_PHYCD_9755 are exactly identical!
WARNING: Duplicate sequences found: 53

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/Q15029/3_mltree/Q15029.raxml.reduced.phy

Alignment comprises 1 partitions and 1614 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 1675 / 1614
Gaps: 42.22 %
Invariant sites: 5.73 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q15029/3_mltree/Q15029.raxml.rba

Parallelization scheme autoconfig: 1 worker(s) x 8 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 / 202 / 16160
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1308480.914004] Initial branch length optimization
[00:00:06 -1121072.391213] Model parameter optimization (eps = 10.000000)
[00:01:16 -1116168.230410] AUTODETECT spr round 1 (radius: 5)
[00:04:19 -735014.217835] AUTODETECT spr round 2 (radius: 10)
[00:07:56 -511773.341931] AUTODETECT spr round 3 (radius: 15)
[00:11:24 -422316.047019] AUTODETECT spr round 4 (radius: 20)
[00:15:38 -393352.614774] AUTODETECT spr round 5 (radius: 25)
[00:20:47 -388286.994239] SPR radius for FAST iterations: 25 (autodetect)
[00:20:47 -388286.994239] Model parameter optimization (eps = 3.000000)
[00:21:19 -387909.922797] FAST spr round 1 (radius: 25)
[00:24:51 -343862.743725] FAST spr round 2 (radius: 25)
[00:27:29 -342185.679240] FAST spr round 3 (radius: 25)
[00:29:49 -342118.035426] FAST spr round 4 (radius: 25)
[00:31:48 -342114.416897] FAST spr round 5 (radius: 25)
[00:33:43 -342114.416896] Model parameter optimization (eps = 1.000000)
[00:34:00 -342106.579976] SLOW spr round 1 (radius: 5)
[00:36:49 -342035.728467] SLOW spr round 2 (radius: 5)
[00:39:31 -342033.485424] SLOW spr round 3 (radius: 5)
[00:42:06 -342033.485388] SLOW spr round 4 (radius: 10)
[00:44:46 -342033.485286] SLOW spr round 5 (radius: 15)
[00:49:23 -342033.485282] SLOW spr round 6 (radius: 20)
[00:55:48 -342033.485282] SLOW spr round 7 (radius: 25)
[01:03:55 -342029.182757] SLOW spr round 8 (radius: 5)
[01:07:41 -342029.182748] SLOW spr round 9 (radius: 10)
[01:11:01 -342029.182748] SLOW spr round 10 (radius: 15)
[01:15:21 -342029.182748] SLOW spr round 11 (radius: 20)
[01:21:51 -342029.182748] SLOW spr round 12 (radius: 25)
[01:29:55 -342029.182748] Model parameter optimization (eps = 0.100000)

[01:30:06] ML tree search #1, logLikelihood: -342029.075277

[01:30:06 -1312355.954798] Initial branch length optimization
[01:30:12 -1127419.369726] Model parameter optimization (eps = 10.000000)
[01:30:55 -1122467.954790] AUTODETECT spr round 1 (radius: 5)
[01:33:58 -747430.351225] AUTODETECT spr round 2 (radius: 10)
[01:37:29 -513934.154784] AUTODETECT spr round 3 (radius: 15)
[01:40:57 -414066.953423] AUTODETECT spr round 4 (radius: 20)
[01:45:03 -388010.315150] AUTODETECT spr round 5 (radius: 25)
[01:50:16 -386260.170383] SPR radius for FAST iterations: 25 (autodetect)
[01:50:16 -386260.170383] Model parameter optimization (eps = 3.000000)
[01:50:39 -385951.427617] FAST spr round 1 (radius: 25)
[01:54:19 -343972.699876] FAST spr round 2 (radius: 25)
[01:57:05 -342203.301956] FAST spr round 3 (radius: 25)
[01:59:22 -342115.912364] FAST spr round 4 (radius: 25)
[02:01:21 -342109.800777] FAST spr round 5 (radius: 25)
[02:03:15 -342109.800704] Model parameter optimization (eps = 1.000000)
[02:03:33 -342096.704220] SLOW spr round 1 (radius: 5)
[02:06:15 -342040.152784] SLOW spr round 2 (radius: 5)
[02:08:55 -342030.499315] SLOW spr round 3 (radius: 5)
[02:11:27 -342030.499299] SLOW spr round 4 (radius: 10)
[02:14:07 -342029.868438] SLOW spr round 5 (radius: 5)
[02:17:37 -342029.867882] SLOW spr round 6 (radius: 10)
[02:20:36 -342029.867882] SLOW spr round 7 (radius: 15)
[02:25:00 -342029.867882] SLOW spr round 8 (radius: 20)
[02:31:30 -342029.867882] SLOW spr round 9 (radius: 25)
[02:39:34 -342026.719678] SLOW spr round 10 (radius: 5)
[02:43:21 -342026.719678] SLOW spr round 11 (radius: 10)
[02:46:40 -342026.719678] SLOW spr round 12 (radius: 15)
[02:51:00 -342026.719678] SLOW spr round 13 (radius: 20)
[02:57:33 -342026.719678] SLOW spr round 14 (radius: 25)
[03:05:36 -342026.719678] Model parameter optimization (eps = 0.100000)

[03:05:54] ML tree search #2, logLikelihood: -342024.958512

[03:05:54 -1307565.658635] Initial branch length optimization
[03:06:00 -1122911.711950] Model parameter optimization (eps = 10.000000)
[03:07:03 -1117884.492539] AUTODETECT spr round 1 (radius: 5)
[03:10:07 -741337.900837] AUTODETECT spr round 2 (radius: 10)
[03:13:44 -486136.268444] AUTODETECT spr round 3 (radius: 15)
[03:17:15 -429663.362400] AUTODETECT spr round 4 (radius: 20)
[03:21:26 -404555.264757] AUTODETECT spr round 5 (radius: 25)
[03:26:29 -395259.104521] SPR radius for FAST iterations: 25 (autodetect)
[03:26:29 -395259.104521] Model parameter optimization (eps = 3.000000)
[03:26:58 -394953.221379] FAST spr round 1 (radius: 25)
[03:30:31 -344203.694550] FAST spr round 2 (radius: 25)
[03:33:07 -342270.264103] FAST spr round 3 (radius: 25)
[03:35:26 -342141.948294] FAST spr round 4 (radius: 25)
[03:37:25 -342140.611689] FAST spr round 5 (radius: 25)
[03:39:19 -342140.611686] Model parameter optimization (eps = 1.000000)
[03:39:48 -342117.489766] SLOW spr round 1 (radius: 5)
[03:42:33 -342069.789268] SLOW spr round 2 (radius: 5)
[03:45:16 -342059.855406] SLOW spr round 3 (radius: 5)
[03:47:53 -342059.257330] SLOW spr round 4 (radius: 5)
[03:50:28 -342059.257285] SLOW spr round 5 (radius: 10)
[03:53:09 -342059.108626] SLOW spr round 6 (radius: 5)
[03:56:38 -342059.108618] SLOW spr round 7 (radius: 10)
[03:59:35 -342059.108617] SLOW spr round 8 (radius: 15)
[04:03:59 -342059.108610] SLOW spr round 9 (radius: 20)
[04:10:29 -342059.108608] SLOW spr round 10 (radius: 25)
[04:18:49 -342054.796874] SLOW spr round 11 (radius: 5)
[04:22:35 -342054.796871] SLOW spr round 12 (radius: 10)
[04:25:55 -342054.796870] SLOW spr round 13 (radius: 15)
[04:30:12 -342054.796868] SLOW spr round 14 (radius: 20)
[04:36:43 -342054.796867] SLOW spr round 15 (radius: 25)
[04:45:01 -342054.796865] Model parameter optimization (eps = 0.100000)

[04:45:14] ML tree search #3, logLikelihood: -342054.714896

[04:45:15 -1315200.357479] Initial branch length optimization
[04:45:20 -1127428.286094] Model parameter optimization (eps = 10.000000)
[04:46:30 -1122453.078978] AUTODETECT spr round 1 (radius: 5)
[04:49:31 -743377.402556] AUTODETECT spr round 2 (radius: 10)
[04:53:09 -484040.004529] AUTODETECT spr round 3 (radius: 15)
[04:56:42 -407819.332195] AUTODETECT spr round 4 (radius: 20)
[05:01:17 -385350.825049] AUTODETECT spr round 5 (radius: 25)
[05:08:06 -383790.511067] SPR radius for FAST iterations: 25 (autodetect)
[05:08:06 -383790.511067] Model parameter optimization (eps = 3.000000)
[05:08:32 -383486.935651] FAST spr round 1 (radius: 25)
[05:12:03 -343697.861023] FAST spr round 2 (radius: 25)
[05:14:40 -342328.011348] FAST spr round 3 (radius: 25)
[05:17:05 -342178.451404] FAST spr round 4 (radius: 25)
[05:19:09 -342139.351957] FAST spr round 5 (radius: 25)
[05:21:06 -342127.323333] FAST spr round 6 (radius: 25)
[05:23:00 -342127.323208] Model parameter optimization (eps = 1.000000)
[05:23:19 -342120.505687] SLOW spr round 1 (radius: 5)
[05:26:03 -342037.545184] SLOW spr round 2 (radius: 5)
[05:28:43 -342036.849660] SLOW spr round 3 (radius: 5)
[05:31:16 -342036.849555] SLOW spr round 4 (radius: 10)
[05:33:57 -342036.224188] SLOW spr round 5 (radius: 5)
[05:37:27 -342036.223583] SLOW spr round 6 (radius: 10)
[05:40:24 -342036.223583] SLOW spr round 7 (radius: 15)
[05:44:51 -342036.223582] SLOW spr round 8 (radius: 20)
[05:51:34 -342031.920136] SLOW spr round 9 (radius: 5)
[05:55:20 -342031.920115] SLOW spr round 10 (radius: 10)
[05:58:35 -342031.920114] SLOW spr round 11 (radius: 15)
[06:02:58 -342031.920114] SLOW spr round 12 (radius: 20)
[06:09:44 -342031.920114] SLOW spr round 13 (radius: 25)
[06:18:10 -342031.920114] Model parameter optimization (eps = 0.100000)

[06:18:25] ML tree search #4, logLikelihood: -342031.789128

[06:18:25 -1313607.245261] Initial branch length optimization
[06:18:32 -1126957.227317] Model parameter optimization (eps = 10.000000)
[06:19:30 -1121995.184206] AUTODETECT spr round 1 (radius: 5)
[06:22:31 -744256.527965] AUTODETECT spr round 2 (radius: 10)
[06:26:07 -506124.676826] AUTODETECT spr round 3 (radius: 15)
[06:29:28 -432915.869763] AUTODETECT spr round 4 (radius: 20)
[06:33:43 -402139.659104] AUTODETECT spr round 5 (radius: 25)
[06:38:39 -394515.244927] SPR radius for FAST iterations: 25 (autodetect)
[06:38:39 -394515.244927] Model parameter optimization (eps = 3.000000)
[06:39:06 -394216.899168] FAST spr round 1 (radius: 25)
[06:42:40 -344709.888749] FAST spr round 2 (radius: 25)
[06:45:28 -342284.915701] FAST spr round 3 (radius: 25)
[06:47:46 -342138.079733] FAST spr round 4 (radius: 25)
[06:49:51 -342126.025189] FAST spr round 5 (radius: 25)
[06:51:46 -342126.025169] Model parameter optimization (eps = 1.000000)
[06:52:02 -342120.209306] SLOW spr round 1 (radius: 5)
[06:54:45 -342048.210704] SLOW spr round 2 (radius: 5)
[06:57:22 -342043.644486] SLOW spr round 3 (radius: 5)
[06:59:58 -342042.843919] SLOW spr round 4 (radius: 5)
[07:02:35 -342039.379506] SLOW spr round 5 (radius: 5)
[07:05:07 -342039.379478] SLOW spr round 6 (radius: 10)
[07:07:49 -342038.742736] SLOW spr round 7 (radius: 5)
[07:11:19 -342038.742225] SLOW spr round 8 (radius: 10)
[07:14:18 -342038.742225] SLOW spr round 9 (radius: 15)
[07:18:44 -342038.742118] SLOW spr round 10 (radius: 20)
[07:25:17 -342035.583552] SLOW spr round 11 (radius: 5)
[07:29:02 -342035.583552] SLOW spr round 12 (radius: 10)
[07:32:18 -342035.583551] SLOW spr round 13 (radius: 15)
[07:36:39 -342035.583551] SLOW spr round 14 (radius: 20)
[07:43:14 -342035.583551] SLOW spr round 15 (radius: 25)
[07:51:26 -342035.583550] Model parameter optimization (eps = 0.100000)

[07:51:33] ML tree search #5, logLikelihood: -342035.548314

[07:51:34 -1302957.588307] Initial branch length optimization
[07:51:39 -1121204.976874] Model parameter optimization (eps = 10.000000)
[07:52:45 -1116443.935475] AUTODETECT spr round 1 (radius: 5)
[07:55:46 -720243.436410] AUTODETECT spr round 2 (radius: 10)
[07:59:17 -496192.371847] AUTODETECT spr round 3 (radius: 15)
[08:02:51 -403917.123549] AUTODETECT spr round 4 (radius: 20)
[08:06:42 -381859.386868] AUTODETECT spr round 5 (radius: 25)
[08:11:16 -380381.735009] SPR radius for FAST iterations: 25 (autodetect)
[08:11:16 -380381.735009] Model parameter optimization (eps = 3.000000)
[08:11:33 -380071.495895] FAST spr round 1 (radius: 25)
[08:15:11 -343131.060391] FAST spr round 2 (radius: 25)
[08:17:54 -342195.772711] FAST spr round 3 (radius: 25)
[08:20:15 -342139.605027] FAST spr round 4 (radius: 25)
[08:22:15 -342129.307445] FAST spr round 5 (radius: 25)
[08:24:09 -342129.307442] Model parameter optimization (eps = 1.000000)
[08:24:25 -342121.603887] SLOW spr round 1 (radius: 5)
[08:27:11 -342066.917811] SLOW spr round 2 (radius: 5)
[08:29:57 -342053.134856] SLOW spr round 3 (radius: 5)
[08:32:34 -342050.616095] SLOW spr round 4 (radius: 5)
[08:35:09 -342048.808203] SLOW spr round 5 (radius: 5)
[08:37:40 -342048.808174] SLOW spr round 6 (radius: 10)
[08:40:21 -342048.174607] SLOW spr round 7 (radius: 5)
[08:43:51 -342048.174047] SLOW spr round 8 (radius: 10)
[08:46:52 -342048.174047] SLOW spr round 9 (radius: 15)
[08:51:14 -342048.174046] SLOW spr round 10 (radius: 20)
[08:57:44 -342044.470330] SLOW spr round 11 (radius: 5)
[09:01:29 -342044.469359] SLOW spr round 12 (radius: 10)
[09:04:49 -342044.468755] SLOW spr round 13 (radius: 15)
[09:09:05 -342044.468755] SLOW spr round 14 (radius: 20)
[09:15:37 -342044.468755] SLOW spr round 15 (radius: 25)
[09:23:47 -342040.167568] SLOW spr round 16 (radius: 5)
[09:27:34 -342040.166793] SLOW spr round 17 (radius: 10)
[09:30:54 -342040.166792] SLOW spr round 18 (radius: 15)
[09:35:11 -342040.166792] SLOW spr round 19 (radius: 20)
[09:41:40 -342040.166792] SLOW spr round 20 (radius: 25)
[09:49:49 -342040.166792] Model parameter optimization (eps = 0.100000)

[09:49:58] ML tree search #6, logLikelihood: -342040.117706

[09:49:58 -1302349.886910] Initial branch length optimization
[09:50:05 -1119147.270228] Model parameter optimization (eps = 10.000000)
[09:50:52 -1114282.559972] AUTODETECT spr round 1 (radius: 5)
[09:53:53 -734996.395647] AUTODETECT spr round 2 (radius: 10)
[09:57:26 -505022.329405] AUTODETECT spr round 3 (radius: 15)
[10:01:04 -417631.285399] AUTODETECT spr round 4 (radius: 20)
[10:05:18 -391049.151740] AUTODETECT spr round 5 (radius: 25)
[10:10:36 -386206.287543] SPR radius for FAST iterations: 25 (autodetect)
[10:10:36 -386206.287543] Model parameter optimization (eps = 3.000000)
[10:10:59 -385896.514206] FAST spr round 1 (radius: 25)
[10:14:32 -343002.664148] FAST spr round 2 (radius: 25)
[10:17:11 -342192.287572] FAST spr round 3 (radius: 25)
[10:19:27 -342138.187648] FAST spr round 4 (radius: 25)
[10:21:29 -342130.557590] FAST spr round 5 (radius: 25)
[10:23:23 -342130.557507] Model parameter optimization (eps = 1.000000)
[10:23:41 -342119.219270] SLOW spr round 1 (radius: 5)
[10:26:30 -342052.120635] SLOW spr round 2 (radius: 5)
[10:29:13 -342045.734180] SLOW spr round 3 (radius: 5)
[10:31:49 -342045.734096] SLOW spr round 4 (radius: 10)
[10:34:30 -342045.734094] SLOW spr round 5 (radius: 15)
[10:39:07 -342045.734092] SLOW spr round 6 (radius: 20)
[10:45:31 -342042.577473] SLOW spr round 7 (radius: 5)
[10:49:16 -342042.577466] SLOW spr round 8 (radius: 10)
[10:52:32 -342042.577464] SLOW spr round 9 (radius: 15)
[10:56:53 -342042.577462] SLOW spr round 10 (radius: 20)
[11:03:25 -342042.577460] SLOW spr round 11 (radius: 25)
[11:11:34 -342042.577458] Model parameter optimization (eps = 0.100000)

[11:11:44] ML tree search #7, logLikelihood: -342042.536317

[11:11:44 -1305086.549558] Initial branch length optimization
[11:11:51 -1120824.562776] Model parameter optimization (eps = 10.000000)
[11:12:49 -1115976.403955] AUTODETECT spr round 1 (radius: 5)
[11:15:52 -720792.319041] AUTODETECT spr round 2 (radius: 10)
[11:19:20 -509699.844779] AUTODETECT spr round 3 (radius: 15)
[11:22:39 -434923.481182] AUTODETECT spr round 4 (radius: 20)
[11:26:34 -393301.260963] AUTODETECT spr round 5 (radius: 25)
[11:31:42 -389502.260985] SPR radius for FAST iterations: 25 (autodetect)
[11:31:42 -389502.260985] Model parameter optimization (eps = 3.000000)
[11:32:03 -389184.066219] FAST spr round 1 (radius: 25)
[11:35:49 -343809.130294] FAST spr round 2 (radius: 25)
[11:38:33 -342235.846954] FAST spr round 3 (radius: 25)
[11:40:53 -342140.537113] FAST spr round 4 (radius: 25)
[11:42:52 -342137.291022] FAST spr round 5 (radius: 25)
[11:44:48 -342134.940863] FAST spr round 6 (radius: 25)
[11:46:42 -342134.940861] Model parameter optimization (eps = 1.000000)
[11:46:57 -342130.079095] SLOW spr round 1 (radius: 5)
[11:49:46 -342055.719485] SLOW spr round 2 (radius: 5)
[11:52:29 -342041.676536] SLOW spr round 3 (radius: 5)
[11:55:04 -342040.880878] SLOW spr round 4 (radius: 5)
[11:57:37 -342040.880796] SLOW spr round 5 (radius: 10)
[12:00:17 -342040.246984] SLOW spr round 6 (radius: 5)
[12:03:47 -342040.246417] SLOW spr round 7 (radius: 10)
[12:06:46 -342040.246417] SLOW spr round 8 (radius: 15)
[12:11:08 -342040.246417] SLOW spr round 9 (radius: 20)
[12:17:36 -342037.093490] SLOW spr round 10 (radius: 5)
[12:21:20 -342037.093477] SLOW spr round 11 (radius: 10)
[12:24:35 -342037.093477] SLOW spr round 12 (radius: 15)
[12:28:53 -342037.093477] SLOW spr round 13 (radius: 20)
[12:35:22 -342037.093477] SLOW spr round 14 (radius: 25)
[12:43:28 -342033.222391] SLOW spr round 15 (radius: 5)
[12:47:16 -342033.222001] SLOW spr round 16 (radius: 10)
[12:50:33 -342033.222001] SLOW spr round 17 (radius: 15)
[12:54:51 -342033.222001] SLOW spr round 18 (radius: 20)
[13:01:18 -342033.222001] SLOW spr round 19 (radius: 25)
[13:09:22 -342033.222001] Model parameter optimization (eps = 0.100000)

[13:09:32] ML tree search #8, logLikelihood: -342033.075820

[13:09:32 -1297807.528141] Initial branch length optimization
[13:09:39 -1110805.983806] Model parameter optimization (eps = 10.000000)
[13:10:40 -1106089.093762] AUTODETECT spr round 1 (radius: 5)
[13:13:41 -728584.935453] AUTODETECT spr round 2 (radius: 10)
[13:17:16 -516290.036284] AUTODETECT spr round 3 (radius: 15)
[13:20:52 -427399.969923] AUTODETECT spr round 4 (radius: 20)
[13:25:29 -397958.405737] AUTODETECT spr round 5 (radius: 25)
[13:30:53 -392176.285036] SPR radius for FAST iterations: 25 (autodetect)
[13:30:53 -392176.285036] Model parameter optimization (eps = 3.000000)
[13:31:19 -391858.024030] FAST spr round 1 (radius: 25)
[13:34:55 -343398.955714] FAST spr round 2 (radius: 25)
[13:37:35 -342269.038205] FAST spr round 3 (radius: 25)
[13:39:54 -342147.600967] FAST spr round 4 (radius: 25)
[13:41:57 -342136.876474] FAST spr round 5 (radius: 25)
[13:43:52 -342136.876467] Model parameter optimization (eps = 1.000000)
[13:44:11 -342129.447075] SLOW spr round 1 (radius: 5)
[13:46:56 -342064.519401] SLOW spr round 2 (radius: 5)
[13:49:38 -342061.216240] SLOW spr round 3 (radius: 5)
[13:52:14 -342061.215849] SLOW spr round 4 (radius: 10)
[13:54:55 -342061.215843] SLOW spr round 5 (radius: 15)
[13:59:32 -342061.215841] SLOW spr round 6 (radius: 20)
[14:06:06 -342056.915407] SLOW spr round 7 (radius: 5)
[14:09:51 -342056.915400] SLOW spr round 8 (radius: 10)
[14:13:09 -342056.915399] SLOW spr round 9 (radius: 15)
[14:17:31 -342056.915397] SLOW spr round 10 (radius: 20)
[14:24:13 -342056.915396] SLOW spr round 11 (radius: 25)
[14:32:45 -342056.915394] Model parameter optimization (eps = 0.100000)

[14:33:01] ML tree search #9, logLikelihood: -342056.838939

[14:33:01 -1311006.176297] Initial branch length optimization
[14:33:07 -1120507.054937] Model parameter optimization (eps = 10.000000)
[14:33:54 -1115685.904108] AUTODETECT spr round 1 (radius: 5)
[14:36:58 -707271.032663] AUTODETECT spr round 2 (radius: 10)
[14:40:27 -508606.739283] AUTODETECT spr round 3 (radius: 15)
[14:43:51 -434206.142536] AUTODETECT spr round 4 (radius: 20)
[14:47:51 -399958.585895] AUTODETECT spr round 5 (radius: 25)
[14:52:33 -391162.014847] SPR radius for FAST iterations: 25 (autodetect)
[14:52:33 -391162.014847] Model parameter optimization (eps = 3.000000)
[14:52:58 -390834.347703] FAST spr round 1 (radius: 25)
[14:56:37 -343342.541035] FAST spr round 2 (radius: 25)
[14:59:12 -342192.805709] FAST spr round 3 (radius: 25)
[15:01:28 -342142.143452] FAST spr round 4 (radius: 25)
[15:03:27 -342139.924885] FAST spr round 5 (radius: 25)
[15:05:23 -342139.924852] Model parameter optimization (eps = 1.000000)
[15:05:38 -342133.647425] SLOW spr round 1 (radius: 5)
[15:08:29 -342048.114999] SLOW spr round 2 (radius: 5)
[15:11:12 -342040.736263] SLOW spr round 3 (radius: 5)
[15:13:48 -342040.736205] SLOW spr round 4 (radius: 10)
[15:16:28 -342040.736201] SLOW spr round 5 (radius: 15)
[15:21:08 -342040.736197] SLOW spr round 6 (radius: 20)
[15:27:37 -342037.576219] SLOW spr round 7 (radius: 5)
[15:31:22 -342037.576207] SLOW spr round 8 (radius: 10)
[15:34:39 -342037.576207] SLOW spr round 9 (radius: 15)
[15:39:00 -342037.576207] SLOW spr round 10 (radius: 20)
[15:45:37 -342037.576207] SLOW spr round 11 (radius: 25)
[15:53:58 -342037.576207] Model parameter optimization (eps = 0.100000)

[15:54:10] ML tree search #10, logLikelihood: -342037.470760

[15:54:10 -1301832.549065] Initial branch length optimization
[15:54:16 -1117254.534099] Model parameter optimization (eps = 10.000000)
[15:55:08 -1112414.912920] AUTODETECT spr round 1 (radius: 5)
[15:58:15 -727926.262184] AUTODETECT spr round 2 (radius: 10)
[16:01:47 -520227.667766] AUTODETECT spr round 3 (radius: 15)
[16:05:18 -420927.523022] AUTODETECT spr round 4 (radius: 20)
[16:09:02 -398357.080826] AUTODETECT spr round 5 (radius: 25)
[16:12:58 -390645.150907] SPR radius for FAST iterations: 25 (autodetect)
[16:12:58 -390645.150907] Model parameter optimization (eps = 3.000000)
[16:13:27 -390347.305671] FAST spr round 1 (radius: 25)
[16:17:02 -343393.592647] FAST spr round 2 (radius: 25)
[16:19:44 -342226.507381] FAST spr round 3 (radius: 25)
[16:22:09 -342160.426387] FAST spr round 4 (radius: 25)
[16:24:11 -342154.435039] FAST spr round 5 (radius: 25)
[16:26:07 -342152.088750] FAST spr round 6 (radius: 25)
[16:28:01 -342152.088749] Model parameter optimization (eps = 1.000000)
[16:28:15 -342148.434423] SLOW spr round 1 (radius: 5)
[16:31:01 -342065.385379] SLOW spr round 2 (radius: 5)
[16:33:42 -342045.784623] SLOW spr round 3 (radius: 5)
[16:36:16 -342042.474049] SLOW spr round 4 (radius: 5)
[16:38:49 -342042.474010] SLOW spr round 5 (radius: 10)
[16:41:31 -342042.243846] SLOW spr round 6 (radius: 5)
[16:45:02 -342042.241885] SLOW spr round 7 (radius: 10)
[16:48:01 -342042.241145] SLOW spr round 8 (radius: 15)
[16:52:29 -342042.241143] SLOW spr round 9 (radius: 20)
[16:59:08 -342037.604086] SLOW spr round 10 (radius: 5)
[17:02:56 -342034.214287] SLOW spr round 11 (radius: 5)
[17:06:09 -342034.213013] SLOW spr round 12 (radius: 10)
[17:08:58 -342034.213013] SLOW spr round 13 (radius: 15)
[17:13:28 -342034.213013] SLOW spr round 14 (radius: 20)
[17:20:01 -342034.213012] SLOW spr round 15 (radius: 25)
[17:28:16 -342034.213012] Model parameter optimization (eps = 0.100000)

[17:28:27] ML tree search #11, logLikelihood: -342033.968618

[17:28:27 -1308906.313746] Initial branch length optimization
[17:28:33 -1120037.814506] Model parameter optimization (eps = 10.000000)
[17:29:21 -1115312.273953] AUTODETECT spr round 1 (radius: 5)
[17:32:26 -739429.658593] AUTODETECT spr round 2 (radius: 10)
[17:35:59 -512794.169141] AUTODETECT spr round 3 (radius: 15)
[17:39:15 -428541.709590] AUTODETECT spr round 4 (radius: 20)
[17:43:31 -394907.459041] AUTODETECT spr round 5 (radius: 25)
[17:48:27 -389400.804449] SPR radius for FAST iterations: 25 (autodetect)
[17:48:27 -389400.804449] Model parameter optimization (eps = 3.000000)
[17:48:50 -389099.928362] FAST spr round 1 (radius: 25)
[17:52:27 -344544.481006] FAST spr round 2 (radius: 25)
[17:55:12 -342209.990520] FAST spr round 3 (radius: 25)
[17:57:30 -342149.901529] FAST spr round 4 (radius: 25)
[17:59:32 -342136.597747] FAST spr round 5 (radius: 25)
[18:01:27 -342136.597746] Model parameter optimization (eps = 1.000000)
[18:01:42 -342128.700280] SLOW spr round 1 (radius: 5)
[18:04:32 -342053.454316] SLOW spr round 2 (radius: 5)
[18:07:15 -342040.913372] SLOW spr round 3 (radius: 5)
[18:09:55 -342039.385337] SLOW spr round 4 (radius: 5)
[18:12:29 -342039.384853] SLOW spr round 5 (radius: 10)
[18:15:10 -342039.384843] SLOW spr round 6 (radius: 15)
[18:19:53 -342039.384835] SLOW spr round 7 (radius: 20)
[18:26:15 -342039.384835] SLOW spr round 8 (radius: 25)
[18:34:27 -342039.384835] Model parameter optimization (eps = 0.100000)

[18:34:34] ML tree search #12, logLikelihood: -342039.289623

[18:34:34 -1315602.053330] Initial branch length optimization
[18:34:42 -1130557.215695] Model parameter optimization (eps = 10.000000)
[18:35:26 -1125764.796713] AUTODETECT spr round 1 (radius: 5)
[18:38:31 -745325.659713] AUTODETECT spr round 2 (radius: 10)
[18:42:07 -500370.767768] AUTODETECT spr round 3 (radius: 15)
[18:45:31 -415147.441139] AUTODETECT spr round 4 (radius: 20)
[18:49:59 -393844.297302] AUTODETECT spr round 5 (radius: 25)
[18:55:44 -386380.475872] SPR radius for FAST iterations: 25 (autodetect)
[18:55:44 -386380.475872] Model parameter optimization (eps = 3.000000)
[18:56:12 -386065.610811] FAST spr round 1 (radius: 25)
[18:59:58 -343988.882275] FAST spr round 2 (radius: 25)
[19:02:45 -342266.893859] FAST spr round 3 (radius: 25)
[19:05:11 -342163.223683] FAST spr round 4 (radius: 25)
[19:07:22 -342134.498095] FAST spr round 5 (radius: 25)
[19:09:22 -342129.880875] FAST spr round 6 (radius: 25)
[19:11:17 -342129.880814] Model parameter optimization (eps = 1.000000)
[19:11:34 -342122.622537] SLOW spr round 1 (radius: 5)
[19:14:27 -342061.717582] SLOW spr round 2 (radius: 5)
[19:17:08 -342060.868681] SLOW spr round 3 (radius: 5)
[19:19:46 -342060.868496] SLOW spr round 4 (radius: 10)
[19:22:28 -342060.868496] SLOW spr round 5 (radius: 15)
[19:27:10 -342060.868488] SLOW spr round 6 (radius: 20)
[19:33:44 -342060.868488] SLOW spr round 7 (radius: 25)
[19:42:03 -342056.555742] SLOW spr round 8 (radius: 5)
[19:45:53 -342056.555707] SLOW spr round 9 (radius: 10)
[19:49:17 -342056.555707] SLOW spr round 10 (radius: 15)
[19:53:39 -342056.555707] SLOW spr round 11 (radius: 20)
[20:00:23 -342056.555707] SLOW spr round 12 (radius: 25)
[20:08:39 -342056.555707] Model parameter optimization (eps = 0.100000)

[20:08:51] ML tree search #13, logLikelihood: -342056.114932

[20:08:51 -1313940.495809] Initial branch length optimization
[20:08:58 -1129249.730747] Model parameter optimization (eps = 10.000000)
[20:09:59 -1124182.406881] AUTODETECT spr round 1 (radius: 5)
[20:13:03 -726937.469048] AUTODETECT spr round 2 (radius: 10)
[20:16:34 -493991.434182] AUTODETECT spr round 3 (radius: 15)
[20:20:12 -406004.084872] AUTODETECT spr round 4 (radius: 20)
[20:24:07 -386939.685158] AUTODETECT spr round 5 (radius: 25)
[20:29:07 -385991.542093] SPR radius for FAST iterations: 25 (autodetect)
[20:29:07 -385991.542093] Model parameter optimization (eps = 3.000000)
[20:29:33 -385646.480585] FAST spr round 1 (radius: 25)
[20:33:04 -343625.561555] FAST spr round 2 (radius: 25)
[20:35:46 -342204.005419] FAST spr round 3 (radius: 25)
[20:38:06 -342125.002051] FAST spr round 4 (radius: 25)
[20:40:07 -342114.319389] FAST spr round 5 (radius: 25)
[20:42:01 -342114.319372] Model parameter optimization (eps = 1.000000)
[20:42:18 -342108.867045] SLOW spr round 1 (radius: 5)
[20:45:01 -342046.630126] SLOW spr round 2 (radius: 5)
[20:47:42 -342042.199941] SLOW spr round 3 (radius: 5)
[20:50:18 -342042.199796] SLOW spr round 4 (radius: 10)
[20:53:00 -342041.566332] SLOW spr round 5 (radius: 5)
[20:56:32 -342041.565797] SLOW spr round 6 (radius: 10)
[20:59:32 -342041.565797] SLOW spr round 7 (radius: 15)
[21:03:56 -342041.565797] SLOW spr round 8 (radius: 20)
[21:10:34 -342037.262844] SLOW spr round 9 (radius: 5)
[21:14:20 -342037.262836] SLOW spr round 10 (radius: 10)
[21:17:38 -342037.262836] SLOW spr round 11 (radius: 15)
[21:21:57 -342037.262836] SLOW spr round 12 (radius: 20)
[21:28:38 -342037.262836] SLOW spr round 13 (radius: 25)
[21:37:01 -342037.262836] Model parameter optimization (eps = 0.100000)

[21:37:10] ML tree search #14, logLikelihood: -342037.222023

[21:37:10 -1306459.179358] Initial branch length optimization
[21:37:18 -1118597.315008] Model parameter optimization (eps = 10.000000)
[21:38:02 -1113899.514053] AUTODETECT spr round 1 (radius: 5)
[21:41:08 -717283.638123] AUTODETECT spr round 2 (radius: 10)
[21:44:41 -494514.888115] AUTODETECT spr round 3 (radius: 15)
[21:48:08 -413076.029249] AUTODETECT spr round 4 (radius: 20)
[21:52:08 -392286.942068] AUTODETECT spr round 5 (radius: 25)
[21:56:30 -387774.488801] SPR radius for FAST iterations: 25 (autodetect)
[21:56:30 -387774.488801] Model parameter optimization (eps = 3.000000)
[21:56:52 -387417.217760] FAST spr round 1 (radius: 25)
[22:00:30 -343361.643237] FAST spr round 2 (radius: 25)
[22:03:08 -342162.469091] FAST spr round 3 (radius: 25)
[22:05:26 -342119.776153] FAST spr round 4 (radius: 25)
[22:07:26 -342117.146264] FAST spr round 5 (radius: 25)
[22:09:22 -342117.146236] Model parameter optimization (eps = 1.000000)
[22:09:39 -342112.538662] SLOW spr round 1 (radius: 5)
[22:12:24 -342048.132203] SLOW spr round 2 (radius: 5)
[22:15:06 -342044.557020] SLOW spr round 3 (radius: 5)
[22:17:41 -342044.556816] SLOW spr round 4 (radius: 10)
[22:20:23 -342044.556810] SLOW spr round 5 (radius: 15)
[22:25:09 -342044.556805] SLOW spr round 6 (radius: 20)
[22:31:48 -342037.543717] SLOW spr round 7 (radius: 5)
[22:35:35 -342037.543621] SLOW spr round 8 (radius: 10)
[22:38:56 -342037.542952] SLOW spr round 9 (radius: 15)
[22:43:23 -342037.542950] SLOW spr round 10 (radius: 20)
[22:50:06 -342037.542947] SLOW spr round 11 (radius: 25)
[22:58:44 -342037.542945] Model parameter optimization (eps = 0.100000)

[22:58:52] ML tree search #15, logLikelihood: -342037.485888

[22:58:52 -1301898.608281] Initial branch length optimization
[22:58:58 -1115614.702601] Model parameter optimization (eps = 10.000000)
[22:59:44 -1111147.159755] AUTODETECT spr round 1 (radius: 5)
[23:02:48 -723886.249558] AUTODETECT spr round 2 (radius: 10)
[23:06:20 -498121.811265] AUTODETECT spr round 3 (radius: 15)
[23:09:46 -421261.252837] AUTODETECT spr round 4 (radius: 20)
[23:13:50 -409256.938642] AUTODETECT spr round 5 (radius: 25)
[23:18:32 -397939.893441] SPR radius for FAST iterations: 25 (autodetect)
[23:18:32 -397939.893441] Model parameter optimization (eps = 3.000000)
[23:18:57 -397632.872364] FAST spr round 1 (radius: 25)
[23:22:41 -343410.159131] FAST spr round 2 (radius: 25)
[23:25:25 -342207.512127] FAST spr round 3 (radius: 25)
[23:27:40 -342164.279257] FAST spr round 4 (radius: 25)
[23:29:39 -342164.279201] Model parameter optimization (eps = 1.000000)
[23:29:53 -342157.221032] SLOW spr round 1 (radius: 5)
[23:32:47 -342055.277367] SLOW spr round 2 (radius: 5)
[23:35:30 -342044.652143] SLOW spr round 3 (radius: 5)
[23:38:07 -342044.651817] SLOW spr round 4 (radius: 10)
[23:40:50 -342044.000786] SLOW spr round 5 (radius: 5)
[23:44:20 -342044.000527] SLOW spr round 6 (radius: 10)
[23:47:21 -342044.000524] SLOW spr round 7 (radius: 15)
[23:51:48 -342044.000522] SLOW spr round 8 (radius: 20)
[23:58:28 -342039.694113] SLOW spr round 9 (radius: 5)
[24:02:15 -342039.694111] SLOW spr round 10 (radius: 10)
[24:05:34 -342039.694109] SLOW spr round 11 (radius: 15)
[24:09:58 -342039.694106] SLOW spr round 12 (radius: 20)
[24:16:43 -342039.694104] SLOW spr round 13 (radius: 25)
[24:25:16 -342039.694102] Model parameter optimization (eps = 0.100000)

[24:25:26] ML tree search #16, logLikelihood: -342039.572147

[24:25:26 -1308907.304482] Initial branch length optimization
[24:25:32 -1123979.281519] Model parameter optimization (eps = 10.000000)
[24:26:31 -1118986.049148] AUTODETECT spr round 1 (radius: 5)
[24:29:38 -744187.702294] AUTODETECT spr round 2 (radius: 10)
[24:33:03 -525809.012905] AUTODETECT spr round 3 (radius: 15)
[24:36:29 -440313.100098] AUTODETECT spr round 4 (radius: 20)
[24:40:48 -396790.902149] AUTODETECT spr round 5 (radius: 25)
[24:45:29 -388714.538618] SPR radius for FAST iterations: 25 (autodetect)
[24:45:29 -388714.538618] Model parameter optimization (eps = 3.000000)
[24:46:04 -388411.213252] FAST spr round 1 (radius: 25)
[24:49:42 -343365.974609] FAST spr round 2 (radius: 25)
[24:52:23 -342213.766754] FAST spr round 3 (radius: 25)
[24:54:45 -342140.223345] FAST spr round 4 (radius: 25)
[24:56:46 -342137.869501] FAST spr round 5 (radius: 25)
[24:58:41 -342137.869501] Model parameter optimization (eps = 1.000000)
[24:58:58 -342129.674424] SLOW spr round 1 (radius: 5)
[25:01:53 -342045.685018] SLOW spr round 2 (radius: 5)
[25:04:42 -342039.362171] SLOW spr round 3 (radius: 5)
[25:07:23 -342038.054598] SLOW spr round 4 (radius: 5)
[25:09:58 -342038.053914] SLOW spr round 5 (radius: 10)
[25:12:38 -342038.053901] SLOW spr round 6 (radius: 15)
[25:17:17 -342038.053898] SLOW spr round 7 (radius: 20)
[25:23:42 -342033.750363] SLOW spr round 8 (radius: 5)
[25:27:28 -342033.750362] SLOW spr round 9 (radius: 10)
[25:30:42 -342033.750362] SLOW spr round 10 (radius: 15)
[25:35:02 -342033.750362] SLOW spr round 11 (radius: 20)
[25:41:33 -342033.750361] SLOW spr round 12 (radius: 25)
[25:49:44 -342033.750361] Model parameter optimization (eps = 0.100000)

[25:49:51] ML tree search #17, logLikelihood: -342033.695182

[25:49:51 -1310806.784749] Initial branch length optimization
[25:49:58 -1126055.050581] Model parameter optimization (eps = 10.000000)
[25:50:49 -1121200.367484] AUTODETECT spr round 1 (radius: 5)
[25:53:54 -737179.629274] AUTODETECT spr round 2 (radius: 10)
[25:57:28 -508629.324338] AUTODETECT spr round 3 (radius: 15)
[26:00:55 -422023.334779] AUTODETECT spr round 4 (radius: 20)
[26:05:30 -399171.003087] AUTODETECT spr round 5 (radius: 25)
[26:10:50 -390729.876964] SPR radius for FAST iterations: 25 (autodetect)
[26:10:50 -390729.876964] Model parameter optimization (eps = 3.000000)
[26:11:11 -390463.827489] FAST spr round 1 (radius: 25)
[26:14:53 -343762.388824] FAST spr round 2 (radius: 25)
[26:17:29 -342268.644830] FAST spr round 3 (radius: 25)
[26:19:49 -342140.048159] FAST spr round 4 (radius: 25)
[26:21:53 -342135.358308] FAST spr round 5 (radius: 25)
[26:23:47 -342135.358303] Model parameter optimization (eps = 1.000000)
[26:24:04 -342128.690413] SLOW spr round 1 (radius: 5)
[26:26:52 -342057.687862] SLOW spr round 2 (radius: 5)
[26:29:36 -342044.544265] SLOW spr round 3 (radius: 5)
[26:32:19 -342037.747112] SLOW spr round 4 (radius: 5)
[26:34:55 -342034.595862] SLOW spr round 5 (radius: 5)
[26:37:29 -342034.595677] SLOW spr round 6 (radius: 10)
[26:40:09 -342034.595668] SLOW spr round 7 (radius: 15)
[26:44:49 -342034.595666] SLOW spr round 8 (radius: 20)
[26:51:17 -342030.291341] SLOW spr round 9 (radius: 5)
[26:55:01 -342030.291339] SLOW spr round 10 (radius: 10)
[26:58:18 -342030.291338] SLOW spr round 11 (radius: 15)
[27:02:40 -342030.291337] SLOW spr round 12 (radius: 20)
[27:09:17 -342030.291336] SLOW spr round 13 (radius: 25)
[27:17:27 -342030.291335] Model parameter optimization (eps = 0.100000)

[27:17:38] ML tree search #18, logLikelihood: -342030.176610

[27:17:38 -1306796.276108] Initial branch length optimization
[27:17:45 -1123531.248954] Model parameter optimization (eps = 10.000000)
[27:18:33 -1118653.033320] AUTODETECT spr round 1 (radius: 5)
[27:21:38 -717636.527395] AUTODETECT spr round 2 (radius: 10)
[27:25:14 -492305.207465] AUTODETECT spr round 3 (radius: 15)
[27:28:40 -412875.207177] AUTODETECT spr round 4 (radius: 20)
[27:32:47 -391587.736891] AUTODETECT spr round 5 (radius: 25)
[27:37:19 -389832.225215] SPR radius for FAST iterations: 25 (autodetect)
[27:37:19 -389832.225215] Model parameter optimization (eps = 3.000000)
[27:37:43 -389468.681390] FAST spr round 1 (radius: 25)
[27:41:13 -344658.612715] FAST spr round 2 (radius: 25)
[27:43:51 -342419.059993] FAST spr round 3 (radius: 25)
[27:46:11 -342136.266590] FAST spr round 4 (radius: 25)
[27:48:18 -342114.812719] FAST spr round 5 (radius: 25)
[27:50:13 -342114.812718] Model parameter optimization (eps = 1.000000)
[27:50:31 -342109.934950] SLOW spr round 1 (radius: 5)
[27:53:20 -342058.857021] SLOW spr round 2 (radius: 5)
[27:56:03 -342047.393233] SLOW spr round 3 (radius: 5)
[27:58:38 -342047.302850] SLOW spr round 4 (radius: 10)
[28:01:20 -342047.302845] SLOW spr round 5 (radius: 15)
[28:05:55 -342047.302836] SLOW spr round 6 (radius: 20)
[28:12:23 -342042.982938] SLOW spr round 7 (radius: 5)
[28:16:08 -342042.982912] SLOW spr round 8 (radius: 10)
[28:19:25 -342042.982912] SLOW spr round 9 (radius: 15)
[28:23:43 -342042.982912] SLOW spr round 10 (radius: 20)
[28:30:20 -342042.982911] SLOW spr round 11 (radius: 25)
[28:38:48 -342042.982911] Model parameter optimization (eps = 0.100000)

[28:38:54] ML tree search #19, logLikelihood: -342042.957081

[28:38:54 -1304455.624597] Initial branch length optimization
[28:39:00 -1120760.025330] Model parameter optimization (eps = 10.000000)
[28:40:08 -1116092.112106] AUTODETECT spr round 1 (radius: 5)
[28:43:09 -711478.083316] AUTODETECT spr round 2 (radius: 10)
[28:46:33 -490880.368731] AUTODETECT spr round 3 (radius: 15)
[28:49:53 -409027.034926] AUTODETECT spr round 4 (radius: 20)
[28:53:50 -397805.821382] AUTODETECT spr round 5 (radius: 25)
[28:58:28 -387002.140562] SPR radius for FAST iterations: 25 (autodetect)
[28:58:28 -387002.140562] Model parameter optimization (eps = 3.000000)
[28:58:40 -386957.571838] FAST spr round 1 (radius: 25)
[29:02:21 -343818.435255] FAST spr round 2 (radius: 25)
[29:05:08 -342402.079324] FAST spr round 3 (radius: 25)
[29:07:27 -342354.344832] FAST spr round 4 (radius: 25)
[29:09:27 -342354.344452] Model parameter optimization (eps = 1.000000)
[29:09:46 -342105.839189] SLOW spr round 1 (radius: 5)
[29:12:39 -342051.712520] SLOW spr round 2 (radius: 5)
[29:15:20 -342050.982784] SLOW spr round 3 (radius: 5)
[29:17:56 -342050.982781] SLOW spr round 4 (radius: 10)
[29:20:37 -342050.342737] SLOW spr round 5 (radius: 5)
[29:24:08 -342050.342456] SLOW spr round 6 (radius: 10)
[29:27:06 -342050.342455] SLOW spr round 7 (radius: 15)
[29:31:30 -342050.342454] SLOW spr round 8 (radius: 20)
[29:38:03 -342050.342454] SLOW spr round 9 (radius: 25)
[29:46:27 -342046.030832] SLOW spr round 10 (radius: 5)
[29:50:15 -342046.030831] SLOW spr round 11 (radius: 10)
[29:53:35 -342046.030830] SLOW spr round 12 (radius: 15)
[29:57:55 -342046.030829] SLOW spr round 13 (radius: 20)
[30:04:29 -342046.030829] SLOW spr round 14 (radius: 25)
[30:12:52 -342046.030828] Model parameter optimization (eps = 0.100000)

[30:13:02] ML tree search #20, logLikelihood: -342045.788640


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.188310,0.301632) (0.294445,0.395814) (0.265311,0.908401) (0.251934,2.324598) 
   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: -342024.958512

AIC score: 688059.917024 / AICc score: 8732119.917024 / BIC score: 698934.171755
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=1675).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q15029/3_mltree/Q15029.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q15029/3_mltree/Q15029.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q15029/3_mltree/Q15029.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q15029/3_mltree/Q15029.raxml.log

Analysis started: 07-Jul-2021 05:24:29 / finished: 08-Jul-2021 11:37:32

Elapsed time: 108782.878 seconds

Consumed energy: 9734.695 Wh (= 49 km in an electric car, or 243 km with an e-scooter!)