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 20:45:18 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P80404/2_msa/P80404_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P80404/3_mltree/P80404 --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/P80404/2_msa/P80404_trimmed_msa.fasta
[00:00:00] Loaded alignment with 899 taxa and 546 sites

WARNING: Sequences tr_E1C8M8_E1C8M8_CHICK_9031 and tr_A0A226PQK0_A0A226PQK0_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A0E1RX90_A0A0E1RX90_COCIM_246410 and tr_A0A0J6Y5Q5_A0A0J6Y5Q5_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6QG76_B6QG76_TALMQ_441960 and tr_A0A093V4Z6_A0A093V4Z6_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_B8NDA6_B8NDA6_ASPFN_332952 and tr_Q2U920_Q2U920_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_B8NDA6_B8NDA6_ASPFN_332952 and tr_A0A0F0I977_A0A0F0I977_ASPPU_1403190 are exactly identical!
WARNING: Sequences tr_B8NDA6_B8NDA6_ASPFN_332952 and tr_A0A1S9DAI9_A0A1S9DAI9_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_H2QAJ4_H2QAJ4_PANTR_9598 and tr_A0A2R8Z657_A0A2R8Z657_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9G810_F9G810_FUSOF_660025 and tr_N4UT02_N4UT02_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9G810_F9G810_FUSOF_660025 and tr_A0A2H3TKM7_A0A2H3TKM7_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_C6HPS1_C6HPS1_AJECH_544712 and tr_F0USN6_F0USN6_AJEC8_544711 are exactly identical!
WARNING: Sequences tr_A0A0K0JG80_A0A0K0JG80_BRUMA_6279 and tr_A0A0R3QYE5_A0A0R3QYE5_9BILA_42155 are exactly identical!
WARNING: Sequences tr_A2R9C8_A2R9C8_ASPNC_425011 and tr_A0A319A6V4_A0A319A6V4_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_G7XSC6_G7XSC6_ASPKW_1033177 and tr_A0A146FXW0_A0A146FXW0_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_G2YH59_G2YH59_BOTF4_999810 and tr_M7TN52_M7TN52_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2SPT0_F2SPT0_TRIRC_559305 and tr_A0A178F4Z0_A0A178F4Z0_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_A0A0D2XDU8_A0A0D2XDU8_FUSO4_426428 and tr_X0D3J5_X0D3J5_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_A0A0D2XDU8_A0A0D2XDU8_FUSO4_426428 and tr_A0A2H3T3Q5_A0A2H3T3Q5_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_A0A0D2XDU8_A0A0D2XDU8_FUSO4_426428 and tr_A0A2H3HE28_A0A2H3HE28_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_A0A0D2XZB1_A0A0D2XZB1_FUSO4_426428 and tr_A0A2H3GJK5_A0A2H3GJK5_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_U3JN19_U3JN19_FICAL_59894 and tr_A0A218UGC1_A0A218UGC1_9PASE_299123 are exactly identical!
WARNING: Sequences tr_S0DU71_S0DU71_GIBF5_1279085 and tr_A0A365MLH0_A0A365MLH0_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_A0A044U032_A0A044U032_ONCVO_6282 and tr_A0A182EDA3_A0A182EDA3_ONCOC_42157 are exactly identical!
WARNING: Sequences tr_A0A0V0WBZ5_A0A0V0WBZ5_9BILA_92179 and tr_A0A0V1KVE2_A0A0V1KVE2_9BILA_6335 are exactly identical!
WARNING: Sequences tr_A0A0V0VD30_A0A0V0VD30_9BILA_181606 and tr_A0A0V1PIV1_A0A0V1PIV1_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V0VD30_A0A0V0VD30_9BILA_181606 and tr_A0A0V0TKD3_A0A0V0TKD3_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A100IQC5_A0A100IQC5_ASPNG_5061 and tr_A0A1L9N524_A0A1L9N524_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A100IQC5_A0A100IQC5_ASPNG_5061 and tr_A0A317VN62_A0A317VN62_9EURO_1448314 are exactly identical!
WARNING: Sequences tr_A0A319CQ33_A0A319CQ33_9EURO_1448315 and tr_A0A2V5IYQ7_A0A2V5IYQ7_9EURO_1450541 are exactly identical!
WARNING: Duplicate sequences found: 28

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/P80404/3_mltree/P80404.raxml.reduced.phy

Alignment comprises 1 partitions and 546 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 546 / 546
Gaps: 14.76 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P80404/3_mltree/P80404.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 899 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 78 / 6240
[00:00:00] Data distribution: max. searches per worker: 20

Starting ML tree search with 20 distinct starting trees

[00:00:00 -630717.476048] Initial branch length optimization
[00:00:02 -540316.212379] Model parameter optimization (eps = 10.000000)
[00:00:21 -539047.138854] AUTODETECT spr round 1 (radius: 5)
[00:01:40 -420615.027725] AUTODETECT spr round 2 (radius: 10)
[00:03:12 -320432.927513] AUTODETECT spr round 3 (radius: 15)
[00:04:55 -272178.612749] AUTODETECT spr round 4 (radius: 20)
[00:06:57 -261617.717344] AUTODETECT spr round 5 (radius: 25)
[00:09:33 -261441.483494] SPR radius for FAST iterations: 25 (autodetect)
[00:09:33 -261441.483494] Model parameter optimization (eps = 3.000000)
[00:09:46 -261370.021137] FAST spr round 1 (radius: 25)
[00:11:48 -234669.154381] FAST spr round 2 (radius: 25)
[00:13:21 -233676.007501] FAST spr round 3 (radius: 25)
[00:14:44 -233599.387595] FAST spr round 4 (radius: 25)
[00:15:54 -233592.285504] FAST spr round 5 (radius: 25)
[00:16:58 -233592.217965] Model parameter optimization (eps = 1.000000)
[00:17:08 -233583.338168] SLOW spr round 1 (radius: 5)
[00:18:38 -233534.144720] SLOW spr round 2 (radius: 5)
[00:20:03 -233529.183392] SLOW spr round 3 (radius: 5)
[00:21:26 -233526.378082] SLOW spr round 4 (radius: 5)
[00:22:47 -233525.998217] SLOW spr round 5 (radius: 5)
[00:24:09 -233525.997651] SLOW spr round 6 (radius: 10)
[00:25:32 -233525.844365] SLOW spr round 7 (radius: 5)
[00:27:14 -233525.844358] SLOW spr round 8 (radius: 10)
[00:28:45 -233525.844354] SLOW spr round 9 (radius: 15)
[00:31:03 -233525.844352] SLOW spr round 10 (radius: 20)
[00:34:42 -233525.844351] SLOW spr round 11 (radius: 25)
[00:39:20 -233525.844350] Model parameter optimization (eps = 0.100000)

[00:39:25] ML tree search #1, logLikelihood: -233525.750933

[00:39:25 -635001.663063] Initial branch length optimization
[00:39:27 -543681.900069] Model parameter optimization (eps = 10.000000)
[00:39:46 -542382.233226] AUTODETECT spr round 1 (radius: 5)
[00:41:06 -423330.273180] AUTODETECT spr round 2 (radius: 10)
[00:42:37 -317857.742070] AUTODETECT spr round 3 (radius: 15)
[00:44:24 -279731.555911] AUTODETECT spr round 4 (radius: 20)
[00:46:20 -265657.974290] AUTODETECT spr round 5 (radius: 25)
[00:48:24 -262985.815162] SPR radius for FAST iterations: 25 (autodetect)
[00:48:24 -262985.815162] Model parameter optimization (eps = 3.000000)
[00:48:40 -262890.979707] FAST spr round 1 (radius: 25)
[00:50:35 -234768.555975] FAST spr round 2 (radius: 25)
[00:51:59 -233719.091645] FAST spr round 3 (radius: 25)
[00:53:14 -233633.355547] FAST spr round 4 (radius: 25)
[00:54:21 -233610.406742] FAST spr round 5 (radius: 25)
[00:55:25 -233605.652179] FAST spr round 6 (radius: 25)
[00:56:27 -233605.651921] Model parameter optimization (eps = 1.000000)
[00:56:39 -233601.942963] SLOW spr round 1 (radius: 5)
[00:58:07 -233554.926955] SLOW spr round 2 (radius: 5)
[00:59:31 -233549.357307] SLOW spr round 3 (radius: 5)
[01:00:53 -233549.356246] SLOW spr round 4 (radius: 10)
[01:02:25 -233548.408321] SLOW spr round 5 (radius: 5)
[01:04:19 -233543.305331] SLOW spr round 6 (radius: 5)
[01:05:59 -233543.305220] SLOW spr round 7 (radius: 10)
[01:07:33 -233543.305185] SLOW spr round 8 (radius: 15)
[01:10:10 -233543.305162] SLOW spr round 9 (radius: 20)
[01:14:02 -233543.305152] SLOW spr round 10 (radius: 25)
[01:18:54 -233543.305146] Model parameter optimization (eps = 0.100000)

[01:19:03] ML tree search #2, logLikelihood: -233543.129533

[01:19:03 -633684.834596] Initial branch length optimization
[01:19:05 -541717.915636] Model parameter optimization (eps = 10.000000)
[01:19:25 -540419.211792] AUTODETECT spr round 1 (radius: 5)
[01:20:52 -418433.743086] AUTODETECT spr round 2 (radius: 10)
[01:22:31 -312041.288356] AUTODETECT spr round 3 (radius: 15)
[01:24:28 -273961.483714] AUTODETECT spr round 4 (radius: 20)
[01:26:33 -260584.229289] AUTODETECT spr round 5 (radius: 25)
[01:29:00 -259881.076692] SPR radius for FAST iterations: 25 (autodetect)
[01:29:00 -259881.076692] Model parameter optimization (eps = 3.000000)
[01:29:21 -259793.395499] FAST spr round 1 (radius: 25)
[01:31:26 -234779.725901] FAST spr round 2 (radius: 25)
[01:33:00 -233689.548515] FAST spr round 3 (radius: 25)
[01:34:25 -233621.556282] FAST spr round 4 (radius: 25)
[01:35:37 -233614.510292] FAST spr round 5 (radius: 25)
[01:36:47 -233612.896447] FAST spr round 6 (radius: 25)
[01:37:53 -233612.895474] Model parameter optimization (eps = 1.000000)
[01:38:05 -233600.477976] SLOW spr round 1 (radius: 5)
[01:39:37 -233554.101841] SLOW spr round 2 (radius: 5)
[01:41:07 -233544.574450] SLOW spr round 3 (radius: 5)
[01:42:33 -233538.110069] SLOW spr round 4 (radius: 5)
[01:43:56 -233538.101753] SLOW spr round 5 (radius: 10)
[01:45:20 -233538.101356] SLOW spr round 6 (radius: 15)
[01:47:50 -233538.101337] SLOW spr round 7 (radius: 20)
[01:51:24 -233529.621011] SLOW spr round 8 (radius: 5)
[01:53:14 -233529.576738] SLOW spr round 9 (radius: 10)
[01:54:52 -233529.575881] SLOW spr round 10 (radius: 15)
[01:57:09 -233529.575630] SLOW spr round 11 (radius: 20)
[02:00:50 -233529.575558] SLOW spr round 12 (radius: 25)
[02:05:19 -233529.575537] Model parameter optimization (eps = 0.100000)

[02:05:21] ML tree search #3, logLikelihood: -233529.575002

[02:05:21 -632593.999881] Initial branch length optimization
[02:05:23 -541895.459507] Model parameter optimization (eps = 10.000000)
[02:05:42 -540629.738510] AUTODETECT spr round 1 (radius: 5)
[02:07:01 -424213.758802] AUTODETECT spr round 2 (radius: 10)
[02:08:37 -314291.831549] AUTODETECT spr round 3 (radius: 15)
[02:10:23 -268908.351065] AUTODETECT spr round 4 (radius: 20)
[02:12:22 -258928.230127] AUTODETECT spr round 5 (radius: 25)
[02:14:53 -258727.940722] SPR radius for FAST iterations: 25 (autodetect)
[02:14:53 -258727.940722] Model parameter optimization (eps = 3.000000)
[02:15:06 -258632.529365] FAST spr round 1 (radius: 25)
[02:17:00 -234448.888135] FAST spr round 2 (radius: 25)
[02:18:28 -233659.909738] FAST spr round 3 (radius: 25)
[02:19:43 -233618.802170] FAST spr round 4 (radius: 25)
[02:20:50 -233611.633740] FAST spr round 5 (radius: 25)
[02:21:54 -233611.633729] Model parameter optimization (eps = 1.000000)
[02:22:05 -233608.023998] SLOW spr round 1 (radius: 5)
[02:23:38 -233545.563763] SLOW spr round 2 (radius: 5)
[02:25:06 -233539.142137] SLOW spr round 3 (radius: 5)
[02:26:30 -233539.141424] SLOW spr round 4 (radius: 10)
[02:27:54 -233539.009900] SLOW spr round 5 (radius: 5)
[02:29:38 -233538.854837] SLOW spr round 6 (radius: 5)
[02:31:10 -233538.853676] SLOW spr round 7 (radius: 10)
[02:32:36 -233538.853118] SLOW spr round 8 (radius: 15)
[02:35:04 -233538.599560] SLOW spr round 9 (radius: 5)
[02:36:51 -233538.556280] SLOW spr round 10 (radius: 10)
[02:38:28 -233538.555368] SLOW spr round 11 (radius: 15)
[02:40:45 -233538.555098] SLOW spr round 12 (radius: 20)
[02:44:32 -233530.082983] SLOW spr round 13 (radius: 5)
[02:46:30 -233530.081861] SLOW spr round 14 (radius: 10)
[02:48:20 -233530.081768] SLOW spr round 15 (radius: 15)
[02:50:49 -233530.081759] SLOW spr round 16 (radius: 20)
[02:54:58 -233530.081758] SLOW spr round 17 (radius: 25)
[03:00:07 -233530.081758] Model parameter optimization (eps = 0.100000)

[03:00:17] ML tree search #4, logLikelihood: -233529.850885

[03:00:17 -633167.053247] Initial branch length optimization
[03:00:19 -541274.964081] Model parameter optimization (eps = 10.000000)
[03:00:38 -539979.403423] AUTODETECT spr round 1 (radius: 5)
[03:02:04 -416702.200001] AUTODETECT spr round 2 (radius: 10)
[03:03:46 -301205.209915] AUTODETECT spr round 3 (radius: 15)
[03:05:35 -279778.334632] AUTODETECT spr round 4 (radius: 20)
[03:07:45 -263763.965984] AUTODETECT spr round 5 (radius: 25)
[03:10:20 -261400.689121] SPR radius for FAST iterations: 25 (autodetect)
[03:10:20 -261400.689121] Model parameter optimization (eps = 3.000000)
[03:10:36 -261322.017796] FAST spr round 1 (radius: 25)
[03:12:36 -234575.136858] FAST spr round 2 (radius: 25)
[03:14:03 -233691.948826] FAST spr round 3 (radius: 25)
[03:15:21 -233619.286643] FAST spr round 4 (radius: 25)
[03:16:33 -233616.152237] FAST spr round 5 (radius: 25)
[03:17:43 -233614.003151] FAST spr round 6 (radius: 25)
[03:18:51 -233614.001851] Model parameter optimization (eps = 1.000000)
[03:19:02 -233608.438971] SLOW spr round 1 (radius: 5)
[03:20:37 -233540.692000] SLOW spr round 2 (radius: 5)
[03:22:10 -233527.924933] SLOW spr round 3 (radius: 5)
[03:23:39 -233525.494366] SLOW spr round 4 (radius: 5)
[03:25:07 -233524.098291] SLOW spr round 5 (radius: 5)
[03:26:35 -233524.098147] SLOW spr round 6 (radius: 10)
[03:28:04 -233524.098142] SLOW spr round 7 (radius: 15)
[03:30:40 -233524.098142] SLOW spr round 8 (radius: 20)
[03:34:31 -233524.098142] SLOW spr round 9 (radius: 25)
[03:39:34 -233524.098142] Model parameter optimization (eps = 0.100000)

[03:39:41] ML tree search #5, logLikelihood: -233523.974783

[03:39:41 -634491.564181] Initial branch length optimization
[03:39:43 -542397.118656] Model parameter optimization (eps = 10.000000)
[03:40:04 -541145.777099] AUTODETECT spr round 1 (radius: 5)
[03:41:29 -421716.664634] AUTODETECT spr round 2 (radius: 10)
[03:43:17 -308608.862294] AUTODETECT spr round 3 (radius: 15)
[03:45:08 -272553.378172] AUTODETECT spr round 4 (radius: 20)
[03:47:17 -259890.837999] AUTODETECT spr round 5 (radius: 25)
[03:50:01 -259037.530351] SPR radius for FAST iterations: 25 (autodetect)
[03:50:01 -259037.530351] Model parameter optimization (eps = 3.000000)
[03:50:17 -258985.025601] FAST spr round 1 (radius: 25)
[03:52:16 -234549.800533] FAST spr round 2 (radius: 25)
[03:53:50 -233738.210744] FAST spr round 3 (radius: 25)
[03:55:13 -233670.596535] FAST spr round 4 (radius: 25)
[03:56:24 -233660.761296] FAST spr round 5 (radius: 25)
[03:57:34 -233657.443011] FAST spr round 6 (radius: 25)
[03:58:41 -233657.442609] Model parameter optimization (eps = 1.000000)
[03:58:57 -233646.262329] SLOW spr round 1 (radius: 5)
[04:00:34 -233580.237472] SLOW spr round 2 (radius: 5)
[04:02:08 -233551.546574] SLOW spr round 3 (radius: 5)
[04:03:37 -233544.530907] SLOW spr round 4 (radius: 5)
[04:05:03 -233544.529670] SLOW spr round 5 (radius: 10)
[04:06:26 -233544.337616] SLOW spr round 6 (radius: 5)
[04:08:16 -233544.337615] SLOW spr round 7 (radius: 10)
[04:09:54 -233544.337615] SLOW spr round 8 (radius: 15)
[04:12:23 -233544.337615] SLOW spr round 9 (radius: 20)
[04:16:24 -233544.337615] SLOW spr round 10 (radius: 25)
[04:21:24 -233544.337615] Model parameter optimization (eps = 0.100000)

[04:21:32] ML tree search #6, logLikelihood: -233543.574207

[04:21:32 -634186.100064] Initial branch length optimization
[04:21:35 -542240.588849] Model parameter optimization (eps = 10.000000)
[04:21:56 -540993.814997] AUTODETECT spr round 1 (radius: 5)
[04:23:20 -417038.468048] AUTODETECT spr round 2 (radius: 10)
[04:25:01 -310129.382336] AUTODETECT spr round 3 (radius: 15)
[04:26:58 -272442.982263] AUTODETECT spr round 4 (radius: 20)
[04:29:11 -257421.365922] AUTODETECT spr round 5 (radius: 25)
[04:32:06 -255226.173438] SPR radius for FAST iterations: 25 (autodetect)
[04:32:06 -255226.173438] Model parameter optimization (eps = 3.000000)
[04:32:21 -255146.645321] FAST spr round 1 (radius: 25)
[04:34:19 -234809.296395] FAST spr round 2 (radius: 25)
[04:35:52 -233695.788168] FAST spr round 3 (radius: 25)
[04:37:08 -233665.392751] FAST spr round 4 (radius: 25)
[04:38:19 -233660.954789] FAST spr round 5 (radius: 25)
[04:39:27 -233660.954362] Model parameter optimization (eps = 1.000000)
[04:39:38 -233658.109460] SLOW spr round 1 (radius: 5)
[04:41:13 -233576.188346] SLOW spr round 2 (radius: 5)
[04:42:45 -233564.706543] SLOW spr round 3 (radius: 5)
[04:44:14 -233562.315187] SLOW spr round 4 (radius: 5)
[04:45:41 -233562.314199] SLOW spr round 5 (radius: 10)
[04:47:11 -233562.091628] SLOW spr round 6 (radius: 5)
[04:49:01 -233562.091205] SLOW spr round 7 (radius: 10)
[04:50:40 -233562.090855] SLOW spr round 8 (radius: 15)
[04:53:09 -233562.090564] SLOW spr round 9 (radius: 20)
[04:57:10 -233553.520518] SLOW spr round 10 (radius: 5)
[04:59:06 -233553.520129] SLOW spr round 11 (radius: 10)
[05:00:53 -233553.519957] SLOW spr round 12 (radius: 15)
[05:03:19 -233553.519821] SLOW spr round 13 (radius: 20)
[05:07:23 -233553.519708] SLOW spr round 14 (radius: 25)
[05:12:15 -233553.519614] Model parameter optimization (eps = 0.100000)

[05:12:18] ML tree search #7, logLikelihood: -233553.474924

[05:12:18 -634719.645283] Initial branch length optimization
[05:12:20 -542390.765261] Model parameter optimization (eps = 10.000000)
[05:12:40 -541119.294651] AUTODETECT spr round 1 (radius: 5)
[05:14:05 -418086.171837] AUTODETECT spr round 2 (radius: 10)
[05:15:45 -311359.569974] AUTODETECT spr round 3 (radius: 15)
[05:17:46 -278930.332257] AUTODETECT spr round 4 (radius: 20)
[05:19:53 -262392.447840] AUTODETECT spr round 5 (radius: 25)
[05:22:19 -261613.428724] SPR radius for FAST iterations: 25 (autodetect)
[05:22:19 -261613.428724] Model parameter optimization (eps = 3.000000)
[05:22:37 -261524.637058] FAST spr round 1 (radius: 25)
[05:24:44 -234374.654308] FAST spr round 2 (radius: 25)
[05:26:18 -233696.639389] FAST spr round 3 (radius: 25)
[05:27:41 -233604.194195] FAST spr round 4 (radius: 25)
[05:28:52 -233602.625569] FAST spr round 5 (radius: 25)
[05:30:00 -233602.625424] Model parameter optimization (eps = 1.000000)
[05:30:09 -233600.952685] SLOW spr round 1 (radius: 5)
[05:31:47 -233532.660876] SLOW spr round 2 (radius: 5)
[05:33:21 -233523.206698] SLOW spr round 3 (radius: 5)
[05:34:54 -233515.514041] SLOW spr round 4 (radius: 5)
[05:36:24 -233513.641889] SLOW spr round 5 (radius: 5)
[05:37:52 -233513.641368] SLOW spr round 6 (radius: 10)
[05:39:21 -233513.464004] SLOW spr round 7 (radius: 5)
[05:41:12 -233513.463998] SLOW spr round 8 (radius: 10)
[05:42:51 -233513.463995] SLOW spr round 9 (radius: 15)
[05:45:19 -233513.227245] SLOW spr round 10 (radius: 5)
[05:47:15 -233513.183092] SLOW spr round 11 (radius: 10)
[05:48:59 -233513.182293] SLOW spr round 12 (radius: 15)
[05:51:24 -233513.182070] SLOW spr round 13 (radius: 20)
[05:55:13 -233513.182008] SLOW spr round 14 (radius: 25)
[05:59:52 -233513.181991] Model parameter optimization (eps = 0.100000)

[06:00:01] ML tree search #8, logLikelihood: -233511.908373

[06:00:01 -633242.061299] Initial branch length optimization
[06:00:03 -542230.869741] Model parameter optimization (eps = 10.000000)
[06:00:25 -540991.540969] AUTODETECT spr round 1 (radius: 5)
[06:01:48 -430319.704527] AUTODETECT spr round 2 (radius: 10)
[06:03:31 -319692.937042] AUTODETECT spr round 3 (radius: 15)
[06:05:17 -278172.389906] AUTODETECT spr round 4 (radius: 20)
[06:07:22 -260491.363048] AUTODETECT spr round 5 (radius: 25)
[06:09:43 -258620.670989] SPR radius for FAST iterations: 25 (autodetect)
[06:09:43 -258620.670989] Model parameter optimization (eps = 3.000000)
[06:09:58 -258528.460923] FAST spr round 1 (radius: 25)
[06:11:53 -234983.870422] FAST spr round 2 (radius: 25)
[06:13:19 -233682.280073] FAST spr round 3 (radius: 25)
[06:14:32 -233622.337700] FAST spr round 4 (radius: 25)
[06:15:37 -233615.495117] FAST spr round 5 (radius: 25)
[06:16:41 -233614.942174] FAST spr round 6 (radius: 25)
[06:17:44 -233614.572406] FAST spr round 7 (radius: 25)
[06:18:45 -233614.572358] Model parameter optimization (eps = 1.000000)
[06:18:56 -233608.672146] SLOW spr round 1 (radius: 5)
[06:20:21 -233563.359203] SLOW spr round 2 (radius: 5)
[06:21:45 -233549.982474] SLOW spr round 3 (radius: 5)
[06:23:06 -233549.750109] SLOW spr round 4 (radius: 5)
[06:24:25 -233549.749358] SLOW spr round 5 (radius: 10)
[06:25:48 -233549.749225] SLOW spr round 6 (radius: 15)
[06:28:12 -233549.749186] SLOW spr round 7 (radius: 20)
[06:31:44 -233540.820817] SLOW spr round 8 (radius: 5)
[06:33:30 -233540.820743] SLOW spr round 9 (radius: 10)
[06:35:06 -233540.820739] SLOW spr round 10 (radius: 15)
[06:37:29 -233540.820737] SLOW spr round 11 (radius: 20)
[06:41:52 -233540.820736] SLOW spr round 12 (radius: 25)
[06:47:26 -233540.820736] Model parameter optimization (eps = 0.100000)

[06:47:32] ML tree search #9, logLikelihood: -233540.779133

[06:47:32 -635152.955156] Initial branch length optimization
[06:47:34 -542419.473028] Model parameter optimization (eps = 10.000000)
[06:48:00 -541142.001062] AUTODETECT spr round 1 (radius: 5)
[06:49:36 -421861.895894] AUTODETECT spr round 2 (radius: 10)
[06:51:28 -329359.611188] AUTODETECT spr round 3 (radius: 15)
[06:53:32 -282860.829265] AUTODETECT spr round 4 (radius: 20)
[06:55:54 -263318.596493] AUTODETECT spr round 5 (radius: 25)
[06:58:50 -262920.509025] SPR radius for FAST iterations: 25 (autodetect)
[06:58:50 -262920.509025] Model parameter optimization (eps = 3.000000)
[06:58:56 -262916.475263] FAST spr round 1 (radius: 25)
[07:00:56 -235177.294946] FAST spr round 2 (radius: 25)
[07:02:21 -233859.457916] FAST spr round 3 (radius: 25)
[07:03:36 -233716.615879] FAST spr round 4 (radius: 25)
[07:04:48 -233693.047086] FAST spr round 5 (radius: 25)
[07:05:51 -233693.047038] Model parameter optimization (eps = 1.000000)
[07:06:06 -233615.140875] SLOW spr round 1 (radius: 5)
[07:07:54 -233554.130340] SLOW spr round 2 (radius: 5)
[07:09:40 -233548.109754] SLOW spr round 3 (radius: 5)
[07:11:25 -233542.406886] SLOW spr round 4 (radius: 5)
[07:13:05 -233542.406763] SLOW spr round 5 (radius: 10)
[07:14:48 -233539.522521] SLOW spr round 6 (radius: 5)
[07:16:52 -233539.166190] SLOW spr round 7 (radius: 5)
[07:18:44 -233539.165574] SLOW spr round 8 (radius: 10)
[07:20:28 -233538.252580] SLOW spr round 9 (radius: 5)
[07:22:34 -233535.555211] SLOW spr round 10 (radius: 5)
[07:24:25 -233535.555199] SLOW spr round 11 (radius: 10)
[07:26:08 -233535.555199] SLOW spr round 12 (radius: 15)
[07:28:54 -233535.555199] SLOW spr round 13 (radius: 20)
[07:32:19 -233534.730898] SLOW spr round 14 (radius: 5)
[07:34:06 -233534.695255] SLOW spr round 15 (radius: 10)
[07:35:43 -233534.693091] SLOW spr round 16 (radius: 15)
[07:37:54 -233534.692516] SLOW spr round 17 (radius: 20)
[07:41:24 -233534.692365] SLOW spr round 18 (radius: 25)
[07:45:44 -233534.692325] Model parameter optimization (eps = 0.100000)

[07:45:48] ML tree search #10, logLikelihood: -233534.608818

[07:45:48 -638410.821127] Initial branch length optimization
[07:45:50 -543886.674632] Model parameter optimization (eps = 10.000000)
[07:46:09 -542551.043411] AUTODETECT spr round 1 (radius: 5)
[07:47:29 -417384.776497] AUTODETECT spr round 2 (radius: 10)
[07:49:00 -319135.250859] AUTODETECT spr round 3 (radius: 15)
[07:50:45 -269443.771934] AUTODETECT spr round 4 (radius: 20)
[07:52:30 -261855.423228] AUTODETECT spr round 5 (radius: 25)
[07:54:31 -260041.711047] SPR radius for FAST iterations: 25 (autodetect)
[07:54:31 -260041.711047] Model parameter optimization (eps = 3.000000)
[07:54:47 -259967.901965] FAST spr round 1 (radius: 25)
[07:56:42 -234775.277961] FAST spr round 2 (radius: 25)
[07:58:06 -233681.062808] FAST spr round 3 (radius: 25)
[07:59:20 -233640.554801] FAST spr round 4 (radius: 25)
[08:00:27 -233628.645324] FAST spr round 5 (radius: 25)
[08:01:32 -233623.979070] FAST spr round 6 (radius: 25)
[08:02:34 -233623.978638] Model parameter optimization (eps = 1.000000)
[08:02:44 -233621.993218] SLOW spr round 1 (radius: 5)
[08:04:13 -233561.404572] SLOW spr round 2 (radius: 5)
[08:05:38 -233558.871528] SLOW spr round 3 (radius: 5)
[08:07:00 -233558.871156] SLOW spr round 4 (radius: 10)
[08:08:24 -233558.144385] SLOW spr round 5 (radius: 5)
[08:10:07 -233557.203410] SLOW spr round 6 (radius: 5)
[08:11:39 -233557.203371] SLOW spr round 7 (radius: 10)
[08:13:05 -233557.203371] SLOW spr round 8 (radius: 15)
[08:15:28 -233557.203370] SLOW spr round 9 (radius: 20)
[08:18:57 -233557.203370] SLOW spr round 10 (radius: 25)
[08:23:18 -233557.203370] Model parameter optimization (eps = 0.100000)

[08:23:25] ML tree search #11, logLikelihood: -233556.872868

[08:23:25 -633910.268533] Initial branch length optimization
[08:23:27 -543260.176723] Model parameter optimization (eps = 10.000000)
[08:23:45 -541978.596497] AUTODETECT spr round 1 (radius: 5)
[08:25:03 -427681.910343] AUTODETECT spr round 2 (radius: 10)
[08:26:36 -327175.061180] AUTODETECT spr round 3 (radius: 15)
[08:28:23 -273048.411159] AUTODETECT spr round 4 (radius: 20)
[08:30:30 -260412.067085] AUTODETECT spr round 5 (radius: 25)
[08:33:15 -260275.932025] SPR radius for FAST iterations: 25 (autodetect)
[08:33:15 -260275.932025] Model parameter optimization (eps = 3.000000)
[08:33:19 -260273.217228] FAST spr round 1 (radius: 25)
[08:35:12 -235365.977747] FAST spr round 2 (radius: 25)
[08:36:37 -233763.336953] FAST spr round 3 (radius: 25)
[08:37:56 -233679.989382] FAST spr round 4 (radius: 25)
[08:39:01 -233677.610622] FAST spr round 5 (radius: 25)
[08:40:03 -233677.609299] Model parameter optimization (eps = 1.000000)
[08:40:14 -233636.684454] SLOW spr round 1 (radius: 5)
[08:41:44 -233568.495265] SLOW spr round 2 (radius: 5)
[08:43:10 -233542.196420] SLOW spr round 3 (radius: 5)
[08:44:33 -233539.443323] SLOW spr round 4 (radius: 5)
[08:45:53 -233539.442131] SLOW spr round 5 (radius: 10)
[08:47:16 -233539.295594] SLOW spr round 6 (radius: 5)
[08:48:57 -233539.295505] SLOW spr round 7 (radius: 10)
[08:50:27 -233539.295430] SLOW spr round 8 (radius: 15)
[08:52:44 -233539.295381] SLOW spr round 9 (radius: 20)
[08:56:29 -233530.908895] SLOW spr round 10 (radius: 5)
[08:58:15 -233530.865701] SLOW spr round 11 (radius: 10)
[08:59:52 -233530.864809] SLOW spr round 12 (radius: 15)
[09:02:06 -233530.864546] SLOW spr round 13 (radius: 20)
[09:05:51 -233530.864469] SLOW spr round 14 (radius: 25)
[09:10:37 -233530.864446] Model parameter optimization (eps = 0.100000)

[09:10:45] ML tree search #12, logLikelihood: -233528.904376

[09:10:45 -637799.394757] Initial branch length optimization
[09:10:47 -544173.180468] Model parameter optimization (eps = 10.000000)
[09:11:12 -542837.488502] AUTODETECT spr round 1 (radius: 5)
[09:12:30 -414253.690669] AUTODETECT spr round 2 (radius: 10)
[09:13:58 -317470.900603] AUTODETECT spr round 3 (radius: 15)
[09:15:43 -266240.988754] AUTODETECT spr round 4 (radius: 20)
[09:17:37 -260627.310723] AUTODETECT spr round 5 (radius: 25)
[09:19:42 -259492.930505] SPR radius for FAST iterations: 25 (autodetect)
[09:19:42 -259492.930505] Model parameter optimization (eps = 3.000000)
[09:19:54 -259423.170899] FAST spr round 1 (radius: 25)
[09:21:43 -234650.873553] FAST spr round 2 (radius: 25)
[09:23:09 -233639.927895] FAST spr round 3 (radius: 25)
[09:24:25 -233587.759064] FAST spr round 4 (radius: 25)
[09:25:30 -233587.279109] FAST spr round 5 (radius: 25)
[09:26:33 -233587.279050] Model parameter optimization (eps = 1.000000)
[09:26:41 -233583.605749] SLOW spr round 1 (radius: 5)
[09:28:13 -233539.142039] SLOW spr round 2 (radius: 5)
[09:29:40 -233528.394169] SLOW spr round 3 (radius: 5)
[09:31:05 -233517.486461] SLOW spr round 4 (radius: 5)
[09:32:26 -233517.486390] SLOW spr round 5 (radius: 10)
[09:33:49 -233517.486385] SLOW spr round 6 (radius: 15)
[09:36:18 -233517.486384] SLOW spr round 7 (radius: 20)
[09:39:54 -233517.486384] SLOW spr round 8 (radius: 25)
[09:44:29 -233517.486384] Model parameter optimization (eps = 0.100000)

[09:44:32] ML tree search #13, logLikelihood: -233517.433906

[09:44:32 -631233.852423] Initial branch length optimization
[09:44:34 -541549.258548] Model parameter optimization (eps = 10.000000)
[09:44:51 -540320.302024] AUTODETECT spr round 1 (radius: 5)
[09:46:09 -422103.551134] AUTODETECT spr round 2 (radius: 10)
[09:47:43 -317378.040279] AUTODETECT spr round 3 (radius: 15)
[09:49:28 -275269.615491] AUTODETECT spr round 4 (radius: 20)
[09:51:31 -262198.933182] AUTODETECT spr round 5 (radius: 25)
[09:54:20 -259219.184949] SPR radius for FAST iterations: 25 (autodetect)
[09:54:20 -259219.184949] Model parameter optimization (eps = 3.000000)
[09:54:33 -259122.671076] FAST spr round 1 (radius: 25)
[09:56:29 -234890.758833] FAST spr round 2 (radius: 25)
[09:57:55 -233695.414987] FAST spr round 3 (radius: 25)
[09:59:09 -233652.828958] FAST spr round 4 (radius: 25)
[10:00:15 -233648.392874] FAST spr round 5 (radius: 25)
[10:01:18 -233648.392706] Model parameter optimization (eps = 1.000000)
[10:01:29 -233643.972296] SLOW spr round 1 (radius: 5)
[10:02:59 -233584.402550] SLOW spr round 2 (radius: 5)
[10:04:25 -233566.569891] SLOW spr round 3 (radius: 5)
[10:05:48 -233563.542543] SLOW spr round 4 (radius: 5)
[10:07:08 -233563.540782] SLOW spr round 5 (radius: 10)
[10:08:31 -233561.992596] SLOW spr round 6 (radius: 5)
[10:10:12 -233560.990290] SLOW spr round 7 (radius: 5)
[10:11:41 -233560.990088] SLOW spr round 8 (radius: 10)
[10:13:05 -233559.555448] SLOW spr round 9 (radius: 5)
[10:14:45 -233559.555396] SLOW spr round 10 (radius: 10)
[10:16:15 -233559.374480] SLOW spr round 11 (radius: 5)
[10:17:54 -233559.374478] SLOW spr round 12 (radius: 10)
[10:19:23 -233559.374477] SLOW spr round 13 (radius: 15)
[10:21:39 -233559.374476] SLOW spr round 14 (radius: 20)
[10:25:12 -233549.841003] SLOW spr round 15 (radius: 5)
[10:26:58 -233549.786830] SLOW spr round 16 (radius: 10)
[10:28:36 -233549.784205] SLOW spr round 17 (radius: 15)
[10:30:50 -233549.783345] SLOW spr round 18 (radius: 20)
[10:34:25 -233549.783066] SLOW spr round 19 (radius: 25)
[10:38:51 -233549.782976] Model parameter optimization (eps = 0.100000)

[10:38:58] ML tree search #14, logLikelihood: -233549.472221

[10:38:58 -633797.814994] Initial branch length optimization
[10:39:00 -542459.042715] Model parameter optimization (eps = 10.000000)
[10:39:17 -541153.053499] AUTODETECT spr round 1 (radius: 5)
[10:40:36 -430346.695705] AUTODETECT spr round 2 (radius: 10)
[10:42:16 -326948.771148] AUTODETECT spr round 3 (radius: 15)
[10:44:00 -279425.903096] AUTODETECT spr round 4 (radius: 20)
[10:46:00 -264391.463248] AUTODETECT spr round 5 (radius: 25)
[10:48:33 -262862.142351] SPR radius for FAST iterations: 25 (autodetect)
[10:48:33 -262862.142351] Model parameter optimization (eps = 3.000000)
[10:48:47 -262817.559581] FAST spr round 1 (radius: 25)
[10:50:46 -235094.914581] FAST spr round 2 (radius: 25)
[10:52:14 -233727.877843] FAST spr round 3 (radius: 25)
[10:53:32 -233623.816738] FAST spr round 4 (radius: 25)
[10:54:39 -233613.351445] FAST spr round 5 (radius: 25)
[10:55:42 -233613.350918] Model parameter optimization (eps = 1.000000)
[10:55:52 -233611.492715] SLOW spr round 1 (radius: 5)
[10:57:23 -233564.445316] SLOW spr round 2 (radius: 5)
[10:58:50 -233548.631758] SLOW spr round 3 (radius: 5)
[11:00:13 -233546.769378] SLOW spr round 4 (radius: 5)
[11:01:34 -233544.904774] SLOW spr round 5 (radius: 5)
[11:02:55 -233544.904742] SLOW spr round 6 (radius: 10)
[11:04:17 -233544.680224] SLOW spr round 7 (radius: 5)
[11:05:59 -233544.680174] SLOW spr round 8 (radius: 10)
[11:07:30 -233544.680174] SLOW spr round 9 (radius: 15)
[11:09:46 -233544.680174] SLOW spr round 10 (radius: 20)
[11:13:23 -233544.680174] SLOW spr round 11 (radius: 25)
[11:17:49 -233544.680174] Model parameter optimization (eps = 0.100000)

[11:17:55] ML tree search #15, logLikelihood: -233544.071927

[11:17:55 -637455.566535] Initial branch length optimization
[11:17:57 -543757.885118] Model parameter optimization (eps = 10.000000)
[11:18:17 -542468.737187] AUTODETECT spr round 1 (radius: 5)
[11:19:35 -426766.242519] AUTODETECT spr round 2 (radius: 10)
[11:21:11 -317386.967801] AUTODETECT spr round 3 (radius: 15)
[11:22:54 -271263.752479] AUTODETECT spr round 4 (radius: 20)
[11:24:56 -262786.307155] AUTODETECT spr round 5 (radius: 25)
[11:27:25 -259251.449763] SPR radius for FAST iterations: 25 (autodetect)
[11:27:26 -259251.449763] Model parameter optimization (eps = 3.000000)
[11:27:43 -259194.203258] FAST spr round 1 (radius: 25)
[11:29:32 -234321.593873] FAST spr round 2 (radius: 25)
[11:30:56 -233691.795632] FAST spr round 3 (radius: 25)
[11:32:12 -233637.884195] FAST spr round 4 (radius: 25)
[11:33:18 -233629.781210] FAST spr round 5 (radius: 25)
[11:34:21 -233629.780193] Model parameter optimization (eps = 1.000000)
[11:34:30 -233624.839896] SLOW spr round 1 (radius: 5)
[11:36:00 -233566.559851] SLOW spr round 2 (radius: 5)
[11:37:27 -233556.573256] SLOW spr round 3 (radius: 5)
[11:38:50 -233551.433289] SLOW spr round 4 (radius: 5)
[11:40:10 -233548.519333] SLOW spr round 5 (radius: 5)
[11:41:26 -233548.519251] SLOW spr round 6 (radius: 10)
[11:42:43 -233548.359880] SLOW spr round 7 (radius: 5)
[11:44:18 -233548.359880] SLOW spr round 8 (radius: 10)
[11:45:44 -233548.359880] SLOW spr round 9 (radius: 15)
[11:47:52 -233548.359880] SLOW spr round 10 (radius: 20)
[11:51:17 -233548.242635] SLOW spr round 11 (radius: 5)
[11:52:57 -233548.196884] SLOW spr round 12 (radius: 10)
[11:54:29 -233548.195211] SLOW spr round 13 (radius: 15)
[11:56:36 -233548.194730] SLOW spr round 14 (radius: 20)
[12:00:02 -233548.194593] SLOW spr round 15 (radius: 25)
[12:04:15 -233548.194553] Model parameter optimization (eps = 0.100000)

[12:04:19] ML tree search #16, logLikelihood: -233548.106713

[12:04:19 -633968.686765] Initial branch length optimization
[12:04:21 -543051.989120] Model parameter optimization (eps = 10.000000)
[12:04:38 -541787.638143] AUTODETECT spr round 1 (radius: 5)
[12:05:50 -429292.657455] AUTODETECT spr round 2 (radius: 10)
[12:07:15 -326552.351989] AUTODETECT spr round 3 (radius: 15)
[12:08:53 -273321.041078] AUTODETECT spr round 4 (radius: 20)
[12:10:32 -263292.672849] AUTODETECT spr round 5 (radius: 25)
[12:12:30 -260331.445051] SPR radius for FAST iterations: 25 (autodetect)
[12:12:30 -260331.445051] Model parameter optimization (eps = 3.000000)
[12:12:43 -260259.722487] FAST spr round 1 (radius: 25)
[12:14:26 -235379.703179] FAST spr round 2 (radius: 25)
[12:15:46 -233759.921367] FAST spr round 3 (radius: 25)
[12:16:56 -233659.428451] FAST spr round 4 (radius: 25)
[12:17:58 -233657.442318] FAST spr round 5 (radius: 25)
[12:18:58 -233654.340452] FAST spr round 6 (radius: 25)
[12:19:56 -233654.340223] Model parameter optimization (eps = 1.000000)
[12:20:07 -233650.337127] SLOW spr round 1 (radius: 5)
[12:21:31 -233567.486955] SLOW spr round 2 (radius: 5)
[12:22:52 -233550.063391] SLOW spr round 3 (radius: 5)
[12:24:08 -233550.062867] SLOW spr round 4 (radius: 10)
[12:25:26 -233547.636054] SLOW spr round 5 (radius: 5)
[12:27:03 -233545.118031] SLOW spr round 6 (radius: 5)
[12:28:28 -233545.117967] SLOW spr round 7 (radius: 10)
[12:29:47 -233543.784932] SLOW spr round 8 (radius: 5)
[12:31:22 -233543.784788] SLOW spr round 9 (radius: 10)
[12:32:46 -233543.784771] SLOW spr round 10 (radius: 15)
[12:34:54 -233543.665167] SLOW spr round 11 (radius: 5)
[12:36:32 -233543.621065] SLOW spr round 12 (radius: 10)
[12:38:01 -233543.620268] SLOW spr round 13 (radius: 15)
[12:40:06 -233543.620046] SLOW spr round 14 (radius: 20)
[12:43:31 -233535.196890] SLOW spr round 15 (radius: 5)
[12:45:12 -233535.195768] SLOW spr round 16 (radius: 10)
[12:46:44 -233535.195675] SLOW spr round 17 (radius: 15)
[12:48:48 -233535.195667] SLOW spr round 18 (radius: 20)
[12:52:14 -233535.195666] SLOW spr round 19 (radius: 25)
[12:56:34 -233535.195666] Model parameter optimization (eps = 0.100000)

[12:56:39] ML tree search #17, logLikelihood: -233535.068234

[12:56:39 -636556.897756] Initial branch length optimization
[12:56:40 -544569.316843] Model parameter optimization (eps = 10.000000)
[12:56:56 -543284.032362] AUTODETECT spr round 1 (radius: 5)
[12:58:10 -419623.399085] AUTODETECT spr round 2 (radius: 10)
[12:59:37 -317302.481120] AUTODETECT spr round 3 (radius: 15)
[13:01:20 -274777.021478] AUTODETECT spr round 4 (radius: 20)
[13:03:14 -260460.190907] AUTODETECT spr round 5 (radius: 25)
[13:05:21 -258297.561853] SPR radius for FAST iterations: 25 (autodetect)
[13:05:22 -258297.561853] Model parameter optimization (eps = 3.000000)
[13:05:37 -258214.486388] FAST spr round 1 (radius: 25)
[13:07:22 -234910.233664] FAST spr round 2 (radius: 25)
[13:08:41 -233654.374387] FAST spr round 3 (radius: 25)
[13:09:49 -233587.624863] FAST spr round 4 (radius: 25)
[13:10:51 -233577.159506] FAST spr round 5 (radius: 25)
[13:11:49 -233577.159448] Model parameter optimization (eps = 1.000000)
[13:11:59 -233574.910774] SLOW spr round 1 (radius: 5)
[13:13:20 -233531.015895] SLOW spr round 2 (radius: 5)
[13:14:39 -233521.778109] SLOW spr round 3 (radius: 5)
[13:15:56 -233521.777567] SLOW spr round 4 (radius: 10)
[13:17:13 -233521.558153] SLOW spr round 5 (radius: 5)
[13:18:47 -233521.558107] SLOW spr round 6 (radius: 10)
[13:20:12 -233521.558080] SLOW spr round 7 (radius: 15)
[13:22:16 -233521.558063] SLOW spr round 8 (radius: 20)
[13:25:35 -233512.578771] SLOW spr round 9 (radius: 5)
[13:27:15 -233512.532878] SLOW spr round 10 (radius: 10)
[13:28:46 -233512.532056] SLOW spr round 11 (radius: 15)
[13:30:49 -233512.531825] SLOW spr round 12 (radius: 20)
[13:34:09 -233512.531761] SLOW spr round 13 (radius: 25)
[13:38:21 -233512.531743] Model parameter optimization (eps = 0.100000)

[13:38:30] ML tree search #18, logLikelihood: -233512.238057

[13:38:30 -637944.632733] Initial branch length optimization
[13:38:32 -543923.689585] Model parameter optimization (eps = 10.000000)
[13:38:51 -542606.370162] AUTODETECT spr round 1 (radius: 5)
[13:40:08 -420927.226817] AUTODETECT spr round 2 (radius: 10)
[13:41:36 -320113.627421] AUTODETECT spr round 3 (radius: 15)
[13:43:17 -278228.898812] AUTODETECT spr round 4 (radius: 20)
[13:45:02 -268311.673314] AUTODETECT spr round 5 (radius: 25)
[13:47:12 -263764.861430] SPR radius for FAST iterations: 25 (autodetect)
[13:47:12 -263764.861430] Model parameter optimization (eps = 3.000000)
[13:47:26 -263665.168053] FAST spr round 1 (radius: 25)
[13:49:14 -234691.066258] FAST spr round 2 (radius: 25)
[13:50:41 -233688.274221] FAST spr round 3 (radius: 25)
[13:51:56 -233630.498686] FAST spr round 4 (radius: 25)
[13:53:00 -233625.181509] FAST spr round 5 (radius: 25)
[13:54:02 -233622.466724] FAST spr round 6 (radius: 25)
[13:55:04 -233622.126812] FAST spr round 7 (radius: 25)
[13:56:06 -233622.125896] Model parameter optimization (eps = 1.000000)
[13:56:15 -233616.424964] SLOW spr round 1 (radius: 5)
[13:57:43 -233559.812865] SLOW spr round 2 (radius: 5)
[13:59:07 -233554.979169] SLOW spr round 3 (radius: 5)
[14:00:29 -233547.878226] SLOW spr round 4 (radius: 5)
[14:01:49 -233547.591505] SLOW spr round 5 (radius: 5)
[14:03:07 -233547.591035] SLOW spr round 6 (radius: 10)
[14:04:29 -233547.365769] SLOW spr round 7 (radius: 5)
[14:06:05 -233547.365754] SLOW spr round 8 (radius: 10)
[14:07:37 -233547.365748] SLOW spr round 9 (radius: 15)
[14:10:05 -233547.142588] SLOW spr round 10 (radius: 5)
[14:12:00 -233547.094485] SLOW spr round 11 (radius: 10)
[14:13:46 -233547.092618] SLOW spr round 12 (radius: 15)
[14:16:13 -233547.092070] SLOW spr round 13 (radius: 20)
[14:20:06 -233538.893397] SLOW spr round 14 (radius: 5)
[14:22:03 -233538.891992] SLOW spr round 15 (radius: 10)
[14:23:51 -233538.891848] SLOW spr round 16 (radius: 15)
[14:26:16 -233538.891833] SLOW spr round 17 (radius: 20)
[14:30:08 -233538.891831] SLOW spr round 18 (radius: 25)
[14:34:52 -233538.891830] Model parameter optimization (eps = 0.100000)

[14:34:58] ML tree search #19, logLikelihood: -233538.546851

[14:34:58 -633555.395915] Initial branch length optimization
[14:35:00 -542344.000891] Model parameter optimization (eps = 10.000000)
[14:35:21 -541043.672535] AUTODETECT spr round 1 (radius: 5)
[14:36:46 -416456.919856] AUTODETECT spr round 2 (radius: 10)
[14:38:28 -308105.838677] AUTODETECT spr round 3 (radius: 15)
[14:40:12 -261923.527292] AUTODETECT spr round 4 (radius: 20)
[14:42:45 -256084.006420] AUTODETECT spr round 5 (radius: 25)
[14:45:26 -255767.953389] SPR radius for FAST iterations: 25 (autodetect)
[14:45:26 -255767.953389] Model parameter optimization (eps = 3.000000)
[14:45:40 -255717.853437] FAST spr round 1 (radius: 25)
[14:47:48 -234644.687191] FAST spr round 2 (radius: 25)
[14:49:24 -233718.475295] FAST spr round 3 (radius: 25)
[14:50:50 -233645.715088] FAST spr round 4 (radius: 25)
[14:52:05 -233618.730633] FAST spr round 5 (radius: 25)
[14:53:16 -233615.044051] FAST spr round 6 (radius: 25)
[14:54:26 -233612.375040] FAST spr round 7 (radius: 25)
[14:55:35 -233610.596337] FAST spr round 8 (radius: 25)
[14:56:43 -233610.596175] Model parameter optimization (eps = 1.000000)
[14:56:55 -233606.112946] SLOW spr round 1 (radius: 5)
[14:58:30 -233556.527850] SLOW spr round 2 (radius: 5)
[15:00:04 -233551.370919] SLOW spr round 3 (radius: 5)
[15:01:34 -233548.555065] SLOW spr round 4 (radius: 5)
[15:03:04 -233548.554945] SLOW spr round 5 (radius: 10)
[15:04:37 -233548.409313] SLOW spr round 6 (radius: 5)
[15:06:30 -233548.409307] SLOW spr round 7 (radius: 10)
[15:08:13 -233548.409307] SLOW spr round 8 (radius: 15)
[15:10:44 -233538.771047] SLOW spr round 9 (radius: 5)
[15:12:42 -233537.796322] SLOW spr round 10 (radius: 5)
[15:14:25 -233537.795307] SLOW spr round 11 (radius: 10)
[15:16:03 -233537.794984] SLOW spr round 12 (radius: 15)
[15:18:40 -233537.794880] SLOW spr round 13 (radius: 20)
[15:22:33 -233537.794847] SLOW spr round 14 (radius: 25)
[15:27:32 -233537.794837] Model parameter optimization (eps = 0.100000)

[15:27:41] ML tree search #20, logLikelihood: -233537.321572


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.191461,0.326603) (0.303406,0.414912) (0.234873,1.015412) (0.270260,2.120512) 
   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: -233511.908373

AIC score: 470625.816746 / AICc score: 6961429.816746 / BIC score: 478374.833521
Free parameters (model + branch lengths): 1801

WARNING: Number of free parameters (K=1801) is larger than alignment size (n=546).
         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/P80404/3_mltree/P80404.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P80404/3_mltree/P80404.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P80404/3_mltree/P80404.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P80404/3_mltree/P80404.raxml.log

Analysis started: 03-Jul-2021 20:45:18 / finished: 04-Jul-2021 12:13:00

Elapsed time: 55661.345 seconds

Consumed energy: 4583.163 Wh (= 23 km in an electric car, or 115 km with an e-scooter!)