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 11:55:25 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IYD8/2_msa/Q8IYD8_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IYD8/3_mltree/Q8IYD8 --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/Q8IYD8/2_msa/Q8IYD8_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 573 sites WARNING: Sequences tr_B6QMY5_B6QMY5_TALMQ_441960 and tr_A0A093V7N4_A0A093V7N4_TALMA_1077442 are exactly identical! WARNING: Sequences tr_A0A179UM45_A0A179UM45_BLAGS_559298 and tr_C5GD04_C5GD04_AJEDR_559297 are exactly identical! WARNING: Sequences tr_F9FPU7_F9FPU7_FUSOF_660025 and tr_N4TP96_N4TP96_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FPU7_F9FPU7_FUSOF_660025 and tr_X0C258_X0C258_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FPU7_F9FPU7_FUSOF_660025 and tr_A0A2H3ST38_A0A2H3ST38_FUSOX_5507 are exactly identical! WARNING: Sequences sp_Q2URJ5_MPH1_ASPOR_510516 and tr_A0A1S9DV66_A0A1S9DV66_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A0E0IZ15_A0A0E0IZ15_ORYNI_4536 and tr_A0A0E0R4Z1_A0A0E0R4Z1_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0IZ15_A0A0E0IZ15_ORYNI_4536 and tr_A0A0E0BG20_A0A0E0BG20_9ORYZ_40148 are exactly identical! WARNING: Sequences sp_A2Q8R2_MPH1_ASPNC_425011 and tr_G3XSC3_G3XSC3_ASPNA_380704 are exactly identical! WARNING: Sequences sp_A2Q8R2_MPH1_ASPNC_425011 and tr_A0A319BLF6_A0A319BLF6_9EURO_1450533 are exactly identical! WARNING: Sequences tr_F6WK00_F6WK00_MACMU_9544 and tr_A0A2K6D3C6_A0A2K6D3C6_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7X9L7_G7X9L7_ASPKW_1033177 and tr_A0A146FNW8_A0A146FNW8_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G2XYW3_G2XYW3_BOTF4_999810 and tr_M7TM09_M7TM09_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_L0P6Z0_L0P6Z0_PNEJ8_1209962 and tr_A0A0W4ZEW9_A0A0W4ZEW9_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_V2Z369_V2Z369_MONRO_1381753 and tr_A0A0W0FY27_A0A0W0FY27_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2QKT9_W2QKT9_PHYPN_761204 and tr_A0A0W8CXS7_A0A0W8CXS7_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A096P5R6_A0A096P5R6_PAPAN_9555 and tr_A0A2K6E2Z6_A0A2K6E2Z6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096P5R6_A0A096P5R6_PAPAN_9555 and tr_A0A2K6AAE6_A0A2K6AAE6_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0F9XJW2_A0A0F9XJW2_TRIHA_5544 and tr_A0A2T4AH46_A0A2T4AH46_TRIHA_983964 are exactly identical! WARNING: Sequences tr_A0A0F8ULB9_A0A0F8ULB9_9EURO_308745 and tr_A0A2T5M4H1_A0A2T5M4H1_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0W8DRF4_A0A0W8DRF4_PHYNI_4790 and tr_W2LQ40_W2LQ40_PHYPR_4792 are exactly identical! WARNING: Duplicate sequences found: 21 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/Q8IYD8/3_mltree/Q8IYD8.raxml.reduced.phy Alignment comprises 1 partitions and 573 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 573 / 573 Gaps: 10.92 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IYD8/3_mltree/Q8IYD8.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 7 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 82 / 6560 [00:00:00] Data distribution: max. searches per worker: 20 Starting ML tree search with 20 distinct starting trees [00:00:00 -972196.177275] Initial branch length optimization [00:00:03 -812870.729147] Model parameter optimization (eps = 10.000000) [00:00:50 -811058.994850] AUTODETECT spr round 1 (radius: 5) [00:02:46 -638807.069206] AUTODETECT spr round 2 (radius: 10) [00:05:01 -487400.872318] AUTODETECT spr round 3 (radius: 15) [00:07:30 -406677.127446] AUTODETECT spr round 4 (radius: 20) [00:10:20 -385038.215237] AUTODETECT spr round 5 (radius: 25) [00:13:46 -378455.665084] SPR radius for FAST iterations: 25 (autodetect) [00:13:46 -378455.665084] Model parameter optimization (eps = 3.000000) [00:13:53 -378448.893260] FAST spr round 1 (radius: 25) [00:16:58 -337237.773725] FAST spr round 2 (radius: 25) [00:19:17 -335927.399923] FAST spr round 3 (radius: 25) [00:21:15 -335761.863327] FAST spr round 4 (radius: 25) [00:22:56 -335750.929163] FAST spr round 5 (radius: 25) [00:24:32 -335744.021308] FAST spr round 6 (radius: 25) [00:26:07 -335741.207301] FAST spr round 7 (radius: 25) [00:27:39 -335741.207005] Model parameter optimization (eps = 1.000000) [00:27:55 -335560.336541] SLOW spr round 1 (radius: 5) [00:30:04 -335480.191570] SLOW spr round 2 (radius: 5) [00:32:07 -335469.664098] SLOW spr round 3 (radius: 5) [00:34:05 -335469.591811] SLOW spr round 4 (radius: 10) [00:36:10 -335468.754573] SLOW spr round 5 (radius: 5) [00:38:38 -335468.749350] SLOW spr round 6 (radius: 10) [00:40:57 -335468.748485] SLOW spr round 7 (radius: 15) [00:44:21 -335468.748344] SLOW spr round 8 (radius: 20) [00:49:42 -335468.748321] SLOW spr round 9 (radius: 25) [00:56:44 -335468.748318] Model parameter optimization (eps = 0.100000) [00:56:56] ML tree search #1, logLikelihood: -335468.160203 [00:56:56 -968628.712785] Initial branch length optimization [00:56:59 -811535.880250] Model parameter optimization (eps = 10.000000) [00:57:37 -809538.841542] AUTODETECT spr round 1 (radius: 5) [00:59:35 -625112.110027] AUTODETECT spr round 2 (radius: 10) [01:01:50 -471210.299966] AUTODETECT spr round 3 (radius: 15) [01:04:11 -408873.852250] AUTODETECT spr round 4 (radius: 20) [01:07:01 -382998.829290] AUTODETECT spr round 5 (radius: 25) [01:10:21 -376213.110265] SPR radius for FAST iterations: 25 (autodetect) [01:10:21 -376213.110265] Model parameter optimization (eps = 3.000000) [01:10:28 -376207.817113] FAST spr round 1 (radius: 25) [01:13:29 -337244.748464] FAST spr round 2 (radius: 25) [01:15:44 -335800.170354] FAST spr round 3 (radius: 25) [01:17:41 -335712.051283] FAST spr round 4 (radius: 25) [01:19:23 -335703.469381] FAST spr round 5 (radius: 25) [01:21:00 -335696.077542] FAST spr round 6 (radius: 25) [01:22:34 -335696.077118] Model parameter optimization (eps = 1.000000) [01:22:48 -335536.685513] SLOW spr round 1 (radius: 5) [01:24:59 -335458.677748] SLOW spr round 2 (radius: 5) [01:27:01 -335454.835156] SLOW spr round 3 (radius: 5) [01:28:58 -335452.639641] SLOW spr round 4 (radius: 5) [01:30:59 -335452.639567] SLOW spr round 5 (radius: 10) [01:33:03 -335450.686072] SLOW spr round 6 (radius: 5) [01:35:30 -335450.678411] SLOW spr round 7 (radius: 10) [01:37:48 -335450.677555] SLOW spr round 8 (radius: 15) [01:41:16 -335450.677455] SLOW spr round 9 (radius: 20) [01:46:49 -335450.677443] SLOW spr round 10 (radius: 25) [01:53:53 -335450.677442] Model parameter optimization (eps = 0.100000) [01:54:01] ML tree search #2, logLikelihood: -335450.213840 [01:54:01 -962404.841273] Initial branch length optimization [01:54:04 -806969.614320] Model parameter optimization (eps = 10.000000) [01:54:46 -805089.318431] AUTODETECT spr round 1 (radius: 5) [01:56:41 -632183.757000] AUTODETECT spr round 2 (radius: 10) [01:58:54 -500076.474774] AUTODETECT spr round 3 (radius: 15) [02:01:25 -419992.254635] AUTODETECT spr round 4 (radius: 20) [02:04:10 -378664.220056] AUTODETECT spr round 5 (radius: 25) [02:07:12 -374168.488445] SPR radius for FAST iterations: 25 (autodetect) [02:07:12 -374168.488445] Model parameter optimization (eps = 3.000000) [02:07:19 -374163.080155] FAST spr round 1 (radius: 25) [02:10:22 -337426.912029] FAST spr round 2 (radius: 25) [02:12:45 -335857.759453] FAST spr round 3 (radius: 25) [02:14:47 -335750.161143] FAST spr round 4 (radius: 25) [02:16:32 -335746.051600] FAST spr round 5 (radius: 25) [02:18:10 -335746.050764] Model parameter optimization (eps = 1.000000) [02:18:27 -335517.428970] SLOW spr round 1 (radius: 5) [02:20:42 -335449.338148] SLOW spr round 2 (radius: 5) [02:22:51 -335444.767277] SLOW spr round 3 (radius: 5) [02:24:56 -335444.766365] SLOW spr round 4 (radius: 10) [02:27:08 -335441.970044] SLOW spr round 5 (radius: 5) [02:29:41 -335440.493938] SLOW spr round 6 (radius: 5) [02:31:58 -335440.492598] SLOW spr round 7 (radius: 10) [02:34:14 -335440.492394] SLOW spr round 8 (radius: 15) [02:37:59 -335440.492345] SLOW spr round 9 (radius: 20) [02:43:45 -335440.492325] SLOW spr round 10 (radius: 25) [02:51:11 -335440.492315] Model parameter optimization (eps = 0.100000) [02:51:22] ML tree search #3, logLikelihood: -335439.949796 [02:51:22 -965808.813370] Initial branch length optimization [02:51:25 -810841.953981] Model parameter optimization (eps = 10.000000) [02:52:01 -808999.080671] AUTODETECT spr round 1 (radius: 5) [02:54:01 -631405.751683] AUTODETECT spr round 2 (radius: 10) [02:56:16 -492956.586877] AUTODETECT spr round 3 (radius: 15) [02:58:44 -442573.747797] AUTODETECT spr round 4 (radius: 20) [03:01:37 -393033.008949] AUTODETECT spr round 5 (radius: 25) [03:04:32 -386891.434802] SPR radius for FAST iterations: 25 (autodetect) [03:04:32 -386891.434802] Model parameter optimization (eps = 3.000000) [03:04:51 -386736.557900] FAST spr round 1 (radius: 25) [03:07:56 -342498.238789] FAST spr round 2 (radius: 25) [03:10:20 -335946.174663] FAST spr round 3 (radius: 25) [03:12:17 -335608.550321] FAST spr round 4 (radius: 25) [03:14:02 -335579.305530] FAST spr round 5 (radius: 25) [03:15:38 -335576.447027] FAST spr round 6 (radius: 25) [03:17:11 -335576.446088] Model parameter optimization (eps = 1.000000) [03:17:18 -335575.165354] SLOW spr round 1 (radius: 5) [03:19:31 -335494.109189] SLOW spr round 2 (radius: 5) [03:21:36 -335478.617105] SLOW spr round 3 (radius: 5) [03:23:43 -335464.765361] SLOW spr round 4 (radius: 5) [03:25:44 -335461.837167] SLOW spr round 5 (radius: 5) [03:27:43 -335461.799142] SLOW spr round 6 (radius: 10) [03:29:48 -335461.797056] SLOW spr round 7 (radius: 15) [03:33:42 -335460.832683] SLOW spr round 8 (radius: 5) [03:36:16 -335460.826993] SLOW spr round 9 (radius: 10) [03:38:44 -335460.826061] SLOW spr round 10 (radius: 15) [03:42:19 -335460.825910] SLOW spr round 11 (radius: 20) [03:48:11 -335460.825886] SLOW spr round 12 (radius: 25) [03:55:23 -335460.825882] Model parameter optimization (eps = 0.100000) [03:55:27] ML tree search #4, logLikelihood: -335460.822021 [03:55:27 -964034.105112] Initial branch length optimization [03:55:30 -807741.199711] Model parameter optimization (eps = 10.000000) [03:56:07 -805951.409363] AUTODETECT spr round 1 (radius: 5) [03:58:03 -634816.150255] AUTODETECT spr round 2 (radius: 10) [04:00:19 -480954.130223] AUTODETECT spr round 3 (radius: 15) [04:02:42 -422082.089836] AUTODETECT spr round 4 (radius: 20) [04:05:41 -377461.466633] AUTODETECT spr round 5 (radius: 25) [04:08:34 -372673.064074] SPR radius for FAST iterations: 25 (autodetect) [04:08:34 -372673.064074] Model parameter optimization (eps = 3.000000) [04:08:53 -372509.838365] FAST spr round 1 (radius: 25) [04:11:49 -337090.930140] FAST spr round 2 (radius: 25) [04:14:01 -335716.672892] FAST spr round 3 (radius: 25) [04:16:00 -335573.769386] FAST spr round 4 (radius: 25) [04:17:41 -335562.724786] FAST spr round 5 (radius: 25) [04:19:18 -335560.624083] FAST spr round 6 (radius: 25) [04:20:52 -335560.516225] FAST spr round 7 (radius: 25) [04:22:25 -335560.516072] Model parameter optimization (eps = 1.000000) [04:22:39 -335545.407443] SLOW spr round 1 (radius: 5) [04:24:47 -335479.549951] SLOW spr round 2 (radius: 5) [04:26:50 -335474.748544] SLOW spr round 3 (radius: 5) [04:28:50 -335474.573247] SLOW spr round 4 (radius: 5) [04:30:50 -335474.573019] SLOW spr round 5 (radius: 10) [04:32:56 -335474.315262] SLOW spr round 6 (radius: 5) [04:35:24 -335471.842360] SLOW spr round 7 (radius: 5) [04:37:31 -335471.841944] SLOW spr round 8 (radius: 10) [04:39:41 -335471.841879] SLOW spr round 9 (radius: 15) [04:43:18 -335471.841849] SLOW spr round 10 (radius: 20) [04:48:52 -335471.841834] SLOW spr round 11 (radius: 25) [04:55:58 -335471.841825] Model parameter optimization (eps = 0.100000) [04:56:15] ML tree search #5, logLikelihood: -335470.659531 [04:56:15 -968120.495836] Initial branch length optimization [04:56:18 -810944.691399] Model parameter optimization (eps = 10.000000) [04:56:55 -809114.270313] AUTODETECT spr round 1 (radius: 5) [04:58:52 -638433.790390] AUTODETECT spr round 2 (radius: 10) [05:01:09 -491772.948679] AUTODETECT spr round 3 (radius: 15) [05:03:37 -413613.156544] AUTODETECT spr round 4 (radius: 20) [05:06:24 -380817.977195] AUTODETECT spr round 5 (radius: 25) [05:09:20 -377959.836960] SPR radius for FAST iterations: 25 (autodetect) [05:09:20 -377959.836960] Model parameter optimization (eps = 3.000000) [05:09:36 -377770.093219] FAST spr round 1 (radius: 25) [05:12:30 -337018.566400] FAST spr round 2 (radius: 25) [05:14:44 -335757.465018] FAST spr round 3 (radius: 25) [05:16:46 -335559.473084] FAST spr round 4 (radius: 25) [05:18:28 -335550.757686] FAST spr round 5 (radius: 25) [05:20:06 -335550.755106] Model parameter optimization (eps = 1.000000) [05:20:19 -335545.261694] SLOW spr round 1 (radius: 5) [05:22:33 -335462.418802] SLOW spr round 2 (radius: 5) [05:24:45 -335444.576319] SLOW spr round 3 (radius: 5) [05:26:51 -335436.900326] SLOW spr round 4 (radius: 5) [05:28:53 -335436.896944] SLOW spr round 5 (radius: 10) [05:31:00 -335436.895287] SLOW spr round 6 (radius: 15) [05:34:53 -335435.705679] SLOW spr round 7 (radius: 5) [05:37:28 -335435.700085] SLOW spr round 8 (radius: 10) [05:39:57 -335435.699170] SLOW spr round 9 (radius: 15) [05:43:30 -335435.699022] SLOW spr round 10 (radius: 20) [05:49:18 -335435.698997] SLOW spr round 11 (radius: 25) [05:56:36 -335435.698992] Model parameter optimization (eps = 0.100000) [05:56:47] ML tree search #6, logLikelihood: -335434.630793 [05:56:47 -969059.755789] Initial branch length optimization [05:56:50 -811793.000907] Model parameter optimization (eps = 10.000000) [05:57:32 -809943.570559] AUTODETECT spr round 1 (radius: 5) [05:59:29 -636280.107915] AUTODETECT spr round 2 (radius: 10) [06:01:41 -489248.885236] AUTODETECT spr round 3 (radius: 15) [06:04:07 -425507.536554] AUTODETECT spr round 4 (radius: 20) [06:06:46 -391447.504135] AUTODETECT spr round 5 (radius: 25) [06:10:19 -383086.700303] SPR radius for FAST iterations: 25 (autodetect) [06:10:19 -383086.700303] Model parameter optimization (eps = 3.000000) [06:10:26 -383081.332491] FAST spr round 1 (radius: 25) [06:13:29 -337851.136453] FAST spr round 2 (radius: 25) [06:15:46 -335870.998699] FAST spr round 3 (radius: 25) [06:17:43 -335763.876765] FAST spr round 4 (radius: 25) [06:19:25 -335746.002457] FAST spr round 5 (radius: 25) [06:21:02 -335737.051491] FAST spr round 6 (radius: 25) [06:22:34 -335737.051080] Model parameter optimization (eps = 1.000000) [06:22:48 -335589.690848] SLOW spr round 1 (radius: 5) [06:24:59 -335502.680360] SLOW spr round 2 (radius: 5) [06:27:05 -335492.159041] SLOW spr round 3 (radius: 5) [06:29:06 -335487.865392] SLOW spr round 4 (radius: 5) [06:31:05 -335486.942765] SLOW spr round 5 (radius: 5) [06:33:03 -335486.942617] SLOW spr round 6 (radius: 10) [06:35:07 -335486.161444] SLOW spr round 7 (radius: 5) [06:37:34 -335486.155433] SLOW spr round 8 (radius: 10) [06:39:53 -335486.029032] SLOW spr round 9 (radius: 5) [06:42:18 -335481.196807] SLOW spr round 10 (radius: 5) [06:44:26 -335481.196766] SLOW spr round 11 (radius: 10) [06:46:35 -335481.196765] SLOW spr round 12 (radius: 15) [06:50:13 -335479.026938] SLOW spr round 13 (radius: 5) [06:52:46 -335478.831947] SLOW spr round 14 (radius: 5) [06:55:00 -335478.830136] SLOW spr round 15 (radius: 10) [06:57:11 -335478.829828] SLOW spr round 16 (radius: 15) [07:00:44 -335478.829701] SLOW spr round 17 (radius: 20) [07:06:18 -335478.829635] SLOW spr round 18 (radius: 25) [07:13:30 -335478.829599] Model parameter optimization (eps = 0.100000) [07:13:41] ML tree search #7, logLikelihood: -335478.455728 [07:13:41 -967010.439675] Initial branch length optimization [07:13:45 -811137.274853] Model parameter optimization (eps = 10.000000) [07:14:31 -809226.802072] AUTODETECT spr round 1 (radius: 5) [07:16:27 -632818.936538] AUTODETECT spr round 2 (radius: 10) [07:18:43 -492208.453582] AUTODETECT spr round 3 (radius: 15) [07:21:20 -411033.247443] AUTODETECT spr round 4 (radius: 20) [07:23:58 -378907.291944] AUTODETECT spr round 5 (radius: 25) [07:27:26 -374061.146074] SPR radius for FAST iterations: 25 (autodetect) [07:27:26 -374061.146074] Model parameter optimization (eps = 3.000000) [07:27:45 -373778.409993] FAST spr round 1 (radius: 25) [07:30:37 -336807.508828] FAST spr round 2 (radius: 25) [07:32:42 -335657.940403] FAST spr round 3 (radius: 25) [07:34:35 -335601.030381] FAST spr round 4 (radius: 25) [07:36:15 -335582.811027] FAST spr round 5 (radius: 25) [07:37:51 -335582.809189] Model parameter optimization (eps = 1.000000) [07:38:05 -335577.048028] SLOW spr round 1 (radius: 5) [07:40:13 -335460.383378] SLOW spr round 2 (radius: 5) [07:42:18 -335452.668762] SLOW spr round 3 (radius: 5) [07:44:17 -335452.440076] SLOW spr round 4 (radius: 5) [07:46:16 -335452.438606] SLOW spr round 5 (radius: 10) [07:48:20 -335451.693062] SLOW spr round 6 (radius: 5) [07:50:49 -335451.689000] SLOW spr round 7 (radius: 10) [07:53:08 -335451.687353] SLOW spr round 8 (radius: 15) [07:56:37 -335451.686495] SLOW spr round 9 (radius: 20) [08:02:15 -335451.686024] SLOW spr round 10 (radius: 25) [08:09:25 -335451.685762] Model parameter optimization (eps = 0.100000) [08:09:31] ML tree search #8, logLikelihood: -335451.603903 [08:09:31 -967378.032187] Initial branch length optimization [08:09:35 -810729.873951] Model parameter optimization (eps = 10.000000) [08:10:15 -808907.571759] AUTODETECT spr round 1 (radius: 5) [08:12:14 -632946.904396] AUTODETECT spr round 2 (radius: 10) [08:14:31 -485347.307126] AUTODETECT spr round 3 (radius: 15) [08:17:02 -421635.121304] AUTODETECT spr round 4 (radius: 20) [08:20:01 -385594.316338] AUTODETECT spr round 5 (radius: 25) [08:23:23 -376317.235430] SPR radius for FAST iterations: 25 (autodetect) [08:23:23 -376317.235430] Model parameter optimization (eps = 3.000000) [08:23:30 -376313.557920] FAST spr round 1 (radius: 25) [08:26:26 -338012.856624] FAST spr round 2 (radius: 25) [08:28:43 -335846.366997] FAST spr round 3 (radius: 25) [08:30:38 -335726.276158] FAST spr round 4 (radius: 25) [08:32:20 -335715.391989] FAST spr round 5 (radius: 25) [08:34:00 -335715.230960] FAST spr round 6 (radius: 25) [08:35:37 -335715.229213] Model parameter optimization (eps = 1.000000) [08:35:42 -335715.112235] SLOW spr round 1 (radius: 5) [08:37:51 -335636.884378] SLOW spr round 2 (radius: 5) [08:39:57 -335627.960528] SLOW spr round 3 (radius: 5) [08:41:59 -335626.303970] SLOW spr round 4 (radius: 5) [08:44:00 -335626.106561] SLOW spr round 5 (radius: 5) [08:46:00 -335626.105360] SLOW spr round 6 (radius: 10) [08:48:04 -335626.104807] SLOW spr round 7 (radius: 15) [08:51:43 -335626.104384] SLOW spr round 8 (radius: 20) [08:57:04 -335626.104048] SLOW spr round 9 (radius: 25) [09:04:01 -335626.103777] Model parameter optimization (eps = 0.100000) [09:04:05] ML tree search #9, logLikelihood: -335626.075863 [09:04:06 -965997.279290] Initial branch length optimization [09:04:09 -810943.961014] Model parameter optimization (eps = 10.000000) [09:04:50 -809087.601756] AUTODETECT spr round 1 (radius: 5) [09:06:50 -623461.954938] AUTODETECT spr round 2 (radius: 10) [09:09:04 -492605.177342] AUTODETECT spr round 3 (radius: 15) [09:11:32 -427025.697758] AUTODETECT spr round 4 (radius: 20) [09:14:24 -389140.099599] AUTODETECT spr round 5 (radius: 25) [09:17:06 -383478.452436] SPR radius for FAST iterations: 25 (autodetect) [09:17:06 -383478.452436] Model parameter optimization (eps = 3.000000) [09:17:29 -383012.236195] FAST spr round 1 (radius: 25) [09:20:23 -337888.581461] FAST spr round 2 (radius: 25) [09:22:37 -335702.329533] FAST spr round 3 (radius: 25) [09:24:36 -335597.008807] FAST spr round 4 (radius: 25) [09:26:19 -335588.570956] FAST spr round 5 (radius: 25) [09:27:55 -335583.351020] FAST spr round 6 (radius: 25) [09:29:30 -335581.572757] FAST spr round 7 (radius: 25) [09:31:02 -335581.572750] Model parameter optimization (eps = 1.000000) [09:31:19 -335575.829580] SLOW spr round 1 (radius: 5) [09:33:30 -335491.820419] SLOW spr round 2 (radius: 5) [09:35:35 -335481.756563] SLOW spr round 3 (radius: 5) [09:37:34 -335481.754606] SLOW spr round 4 (radius: 10) [09:39:39 -335479.456269] SLOW spr round 5 (radius: 5) [09:42:06 -335479.447909] SLOW spr round 6 (radius: 10) [09:44:24 -335479.446662] SLOW spr round 7 (radius: 15) [09:47:48 -335479.446434] SLOW spr round 8 (radius: 20) [09:53:02 -335479.446374] SLOW spr round 9 (radius: 25) [09:59:44 -335479.446351] Model parameter optimization (eps = 0.100000) [09:59:52] ML tree search #10, logLikelihood: -335479.249575 [09:59:52 -963032.306408] Initial branch length optimization [09:59:55 -806612.468170] Model parameter optimization (eps = 10.000000) [10:00:36 -804816.781739] AUTODETECT spr round 1 (radius: 5) [10:02:31 -634279.741636] AUTODETECT spr round 2 (radius: 10) [10:04:42 -507249.506729] AUTODETECT spr round 3 (radius: 15) [10:07:19 -409908.074739] AUTODETECT spr round 4 (radius: 20) [10:09:50 -387197.368513] AUTODETECT spr round 5 (radius: 25) [10:12:40 -383038.755609] SPR radius for FAST iterations: 25 (autodetect) [10:12:40 -383038.755609] Model parameter optimization (eps = 3.000000) [10:12:57 -382848.593861] FAST spr round 1 (radius: 25) [10:15:50 -337195.000354] FAST spr round 2 (radius: 25) [10:18:06 -335704.282725] FAST spr round 3 (radius: 25) [10:20:01 -335583.933912] FAST spr round 4 (radius: 25) [10:21:49 -335555.673964] FAST spr round 5 (radius: 25) [10:23:25 -335551.867215] FAST spr round 6 (radius: 25) [10:24:59 -335551.865340] Model parameter optimization (eps = 1.000000) [10:25:15 -335547.343204] SLOW spr round 1 (radius: 5) [10:27:24 -335489.993030] SLOW spr round 2 (radius: 5) [10:29:21 -335469.808914] SLOW spr round 3 (radius: 5) [10:31:05 -335465.698558] SLOW spr round 4 (radius: 5) [10:33:01 -335465.154880] SLOW spr round 5 (radius: 5) [10:35:00 -335463.003988] SLOW spr round 6 (radius: 5) [10:36:53 -335463.003840] SLOW spr round 7 (radius: 10) [10:38:51 -335461.079084] SLOW spr round 8 (radius: 5) [10:41:15 -335461.073307] SLOW spr round 9 (radius: 10) [10:43:30 -335460.562553] SLOW spr round 10 (radius: 5) [10:45:47 -335457.296023] SLOW spr round 11 (radius: 5) [10:47:51 -335457.293811] SLOW spr round 12 (radius: 10) [10:49:53 -335457.293543] SLOW spr round 13 (radius: 15) [10:53:21 -335457.293461] SLOW spr round 14 (radius: 20) [10:58:26 -335457.293413] SLOW spr round 15 (radius: 25) [11:05:10 -335457.293381] Model parameter optimization (eps = 0.100000) [11:05:22] ML tree search #11, logLikelihood: -335455.996448 [11:05:22 -967045.227788] Initial branch length optimization [11:05:24 -812049.984895] Model parameter optimization (eps = 10.000000) [11:06:05 -810209.464105] AUTODETECT spr round 1 (radius: 5) [11:07:58 -630094.714559] AUTODETECT spr round 2 (radius: 10) [11:10:09 -483154.061042] AUTODETECT spr round 3 (radius: 15) [11:12:34 -401058.714305] AUTODETECT spr round 4 (radius: 20) [11:15:20 -372105.276276] AUTODETECT spr round 5 (radius: 25) [11:18:13 -369140.471363] SPR radius for FAST iterations: 25 (autodetect) [11:18:13 -369140.471363] Model parameter optimization (eps = 3.000000) [11:18:33 -368973.368676] FAST spr round 1 (radius: 25) [11:21:13 -337073.088031] FAST spr round 2 (radius: 25) [11:23:20 -335857.453701] FAST spr round 3 (radius: 25) [11:25:11 -335605.544821] FAST spr round 4 (radius: 25) [11:26:49 -335540.838124] FAST spr round 5 (radius: 25) [11:28:23 -335540.838030] Model parameter optimization (eps = 1.000000) [11:28:38 -335532.512119] SLOW spr round 1 (radius: 5) [11:30:43 -335459.560192] SLOW spr round 2 (radius: 5) [11:32:45 -335445.002842] SLOW spr round 3 (radius: 5) [11:34:38 -335444.139538] SLOW spr round 4 (radius: 5) [11:36:30 -335444.101995] SLOW spr round 5 (radius: 10) [11:38:31 -335444.099509] SLOW spr round 6 (radius: 15) [11:42:09 -335442.933717] SLOW spr round 7 (radius: 5) [11:44:33 -335442.928665] SLOW spr round 8 (radius: 10) [11:46:52 -335442.927857] SLOW spr round 9 (radius: 15) [11:50:13 -335442.927729] SLOW spr round 10 (radius: 20) [11:55:40 -335442.927709] SLOW spr round 11 (radius: 25) [12:02:34 -335442.927706] Model parameter optimization (eps = 0.100000) [12:02:43] ML tree search #12, logLikelihood: -335442.679015 [12:02:43 -963362.997607] Initial branch length optimization [12:02:46 -810775.198969] Model parameter optimization (eps = 10.000000) [12:03:23 -808915.819231] AUTODETECT spr round 1 (radius: 5) [12:05:15 -635547.979588] AUTODETECT spr round 2 (radius: 10) [12:07:20 -483463.795630] AUTODETECT spr round 3 (radius: 15) [12:09:37 -413730.763085] AUTODETECT spr round 4 (radius: 20) [12:12:26 -383788.437114] AUTODETECT spr round 5 (radius: 25) [12:15:21 -380358.998391] SPR radius for FAST iterations: 25 (autodetect) [12:15:21 -380358.998391] Model parameter optimization (eps = 3.000000) [12:15:38 -380175.532214] FAST spr round 1 (radius: 25) [12:18:31 -337632.726075] FAST spr round 2 (radius: 25) [12:20:37 -335612.365448] FAST spr round 3 (radius: 25) [12:22:26 -335568.652060] FAST spr round 4 (radius: 25) [12:24:06 -335550.557873] FAST spr round 5 (radius: 25) [12:25:43 -335546.748864] FAST spr round 6 (radius: 25) [12:27:16 -335545.393998] FAST spr round 7 (radius: 25) [12:28:46 -335544.479084] FAST spr round 8 (radius: 25) [12:30:14 -335544.477270] Model parameter optimization (eps = 1.000000) [12:30:26 -335540.423883] SLOW spr round 1 (radius: 5) [12:32:29 -335454.613566] SLOW spr round 2 (radius: 5) [12:34:27 -335446.571033] SLOW spr round 3 (radius: 5) [12:36:21 -335446.568586] SLOW spr round 4 (radius: 10) [12:38:19 -335446.567918] SLOW spr round 5 (radius: 15) [12:41:53 -335446.567639] SLOW spr round 6 (radius: 20) [12:47:05 -335446.567500] SLOW spr round 7 (radius: 25) [12:53:44 -335446.567428] Model parameter optimization (eps = 0.100000) [12:53:54] ML tree search #13, logLikelihood: -335446.048436 [12:53:55 -964175.581871] Initial branch length optimization [12:53:58 -810069.552474] Model parameter optimization (eps = 10.000000) [12:54:32 -808389.488822] AUTODETECT spr round 1 (radius: 5) [12:56:23 -633109.887780] AUTODETECT spr round 2 (radius: 10) [12:58:28 -501650.357612] AUTODETECT spr round 3 (radius: 15) [13:00:49 -435995.059610] AUTODETECT spr round 4 (radius: 20) [13:03:34 -414428.787347] AUTODETECT spr round 5 (radius: 25) [13:06:29 -398570.070720] SPR radius for FAST iterations: 25 (autodetect) [13:06:29 -398570.070720] Model parameter optimization (eps = 3.000000) [13:06:47 -398389.461808] FAST spr round 1 (radius: 25) [13:09:36 -347385.989012] FAST spr round 2 (radius: 25) [13:11:51 -336046.059061] FAST spr round 3 (radius: 25) [13:13:46 -335624.302505] FAST spr round 4 (radius: 25) [13:15:25 -335580.532162] FAST spr round 5 (radius: 25) [13:17:00 -335569.033287] FAST spr round 6 (radius: 25) [13:18:32 -335566.633248] FAST spr round 7 (radius: 25) [13:20:04 -335566.633104] Model parameter optimization (eps = 1.000000) [13:20:21 -335561.675643] SLOW spr round 1 (radius: 5) [13:22:22 -335474.638210] SLOW spr round 2 (radius: 5) [13:24:19 -335462.765882] SLOW spr round 3 (radius: 5) [13:26:11 -335460.880783] SLOW spr round 4 (radius: 5) [13:28:03 -335459.598807] SLOW spr round 5 (radius: 5) [13:29:54 -335459.540007] SLOW spr round 6 (radius: 10) [13:31:54 -335459.538111] SLOW spr round 7 (radius: 15) [13:35:25 -335459.166209] SLOW spr round 8 (radius: 5) [13:37:46 -335459.166202] SLOW spr round 9 (radius: 10) [13:39:57 -335459.166201] SLOW spr round 10 (radius: 15) [13:43:11 -335459.166201] SLOW spr round 11 (radius: 20) [13:48:13 -335459.166201] SLOW spr round 12 (radius: 25) [13:54:37 -335459.166201] Model parameter optimization (eps = 0.100000) [13:54:51] ML tree search #14, logLikelihood: -335458.152015 [13:54:51 -967438.124608] Initial branch length optimization [13:54:54 -812306.111902] Model parameter optimization (eps = 10.000000) [13:55:25 -810484.368458] AUTODETECT spr round 1 (radius: 5) [13:57:29 -637619.531682] AUTODETECT spr round 2 (radius: 10) [13:59:40 -503142.545722] AUTODETECT spr round 3 (radius: 15) [14:02:12 -408521.354854] AUTODETECT spr round 4 (radius: 20) [14:05:08 -380798.322995] AUTODETECT spr round 5 (radius: 25) [14:08:10 -377137.294678] SPR radius for FAST iterations: 25 (autodetect) [14:08:10 -377137.294678] Model parameter optimization (eps = 3.000000) [14:08:16 -377134.541226] FAST spr round 1 (radius: 25) [14:11:01 -337091.195159] FAST spr round 2 (radius: 25) [14:13:16 -335791.249293] FAST spr round 3 (radius: 25) [14:15:18 -335746.932400] FAST spr round 4 (radius: 25) [14:17:04 -335736.385769] FAST spr round 5 (radius: 25) [14:18:45 -335730.004532] FAST spr round 6 (radius: 25) [14:20:24 -335726.903497] FAST spr round 7 (radius: 25) [14:22:00 -335726.903313] Model parameter optimization (eps = 1.000000) [14:22:15 -335559.458503] SLOW spr round 1 (radius: 5) [14:24:21 -335475.685221] SLOW spr round 2 (radius: 5) [14:26:22 -335464.037824] SLOW spr round 3 (radius: 5) [14:28:23 -335463.120636] SLOW spr round 4 (radius: 5) [14:30:28 -335463.120491] SLOW spr round 5 (radius: 10) [14:32:35 -335463.120430] SLOW spr round 6 (radius: 15) [14:36:18 -335459.576598] SLOW spr round 7 (radius: 5) [14:38:53 -335459.535698] SLOW spr round 8 (radius: 10) [14:41:20 -335459.535154] SLOW spr round 9 (radius: 15) [14:44:44 -335459.534886] SLOW spr round 10 (radius: 20) [14:49:53 -335459.058772] SLOW spr round 11 (radius: 5) [14:52:20 -335458.926553] SLOW spr round 12 (radius: 5) [14:54:30 -335458.923197] SLOW spr round 13 (radius: 10) [14:56:37 -335458.920992] SLOW spr round 14 (radius: 15) [14:59:58 -335458.919558] SLOW spr round 15 (radius: 20) [15:05:01 -335457.050470] SLOW spr round 16 (radius: 5) [15:07:31 -335457.050376] SLOW spr round 17 (radius: 10) [15:09:53 -335450.808201] SLOW spr round 18 (radius: 5) [15:12:12 -335448.194790] SLOW spr round 19 (radius: 5) [15:14:21 -335447.704928] SLOW spr round 20 (radius: 5) [15:16:21 -335447.704656] SLOW spr round 21 (radius: 10) [15:18:22 -335447.704511] SLOW spr round 22 (radius: 15) [15:21:49 -335447.704433] SLOW spr round 23 (radius: 20) [15:26:49 -335447.704390] SLOW spr round 24 (radius: 25) [15:33:18 -335447.704367] Model parameter optimization (eps = 0.100000) [15:33:30] ML tree search #15, logLikelihood: -335446.693154 [15:33:30 -971316.602399] Initial branch length optimization [15:33:33 -813754.898665] Model parameter optimization (eps = 10.000000) [15:34:09 -811869.177708] AUTODETECT spr round 1 (radius: 5) [15:35:58 -630525.704540] AUTODETECT spr round 2 (radius: 10) [15:38:09 -491392.438994] AUTODETECT spr round 3 (radius: 15) [15:40:39 -418333.973334] AUTODETECT spr round 4 (radius: 20) [15:43:40 -393886.780192] AUTODETECT spr round 5 (radius: 25) [15:46:35 -387030.422818] SPR radius for FAST iterations: 25 (autodetect) [15:46:35 -387030.422818] Model parameter optimization (eps = 3.000000) [15:46:57 -386767.938068] FAST spr round 1 (radius: 25) [15:49:48 -337469.265055] FAST spr round 2 (radius: 25) [15:51:52 -335855.028094] FAST spr round 3 (radius: 25) [15:53:41 -335580.090024] FAST spr round 4 (radius: 25) [15:55:18 -335567.647219] FAST spr round 5 (radius: 25) [15:56:49 -335567.646168] Model parameter optimization (eps = 1.000000) [15:57:04 -335550.415709] SLOW spr round 1 (radius: 5) [15:59:10 -335472.052672] SLOW spr round 2 (radius: 5) [16:01:10 -335467.667935] SLOW spr round 3 (radius: 5) [16:03:03 -335467.279418] SLOW spr round 4 (radius: 5) [16:04:56 -335467.278866] SLOW spr round 5 (radius: 10) [16:06:56 -335465.170418] SLOW spr round 6 (radius: 5) [16:09:16 -335463.882455] SLOW spr round 7 (radius: 5) [16:11:21 -335463.881330] SLOW spr round 8 (radius: 10) [16:13:26 -335463.881161] SLOW spr round 9 (radius: 15) [16:16:51 -335463.881132] SLOW spr round 10 (radius: 20) [16:21:59 -335463.881125] SLOW spr round 11 (radius: 25) [16:28:42 -335463.881122] Model parameter optimization (eps = 0.100000) [16:28:51] ML tree search #16, logLikelihood: -335463.407414 [16:28:51 -962699.788569] Initial branch length optimization [16:28:55 -807779.940675] Model parameter optimization (eps = 10.000000) [16:29:39 -805954.202825] AUTODETECT spr round 1 (radius: 5) [16:31:32 -638410.363873] AUTODETECT spr round 2 (radius: 10) [16:33:44 -479997.970292] AUTODETECT spr round 3 (radius: 15) [16:36:00 -436628.771603] AUTODETECT spr round 4 (radius: 20) [16:38:41 -393301.372175] AUTODETECT spr round 5 (radius: 25) [16:41:32 -387612.555942] SPR radius for FAST iterations: 25 (autodetect) [16:41:32 -387612.555942] Model parameter optimization (eps = 3.000000) [16:41:38 -387608.006682] FAST spr round 1 (radius: 25) [16:44:34 -337503.926158] FAST spr round 2 (radius: 25) [16:46:42 -335878.918813] FAST spr round 3 (radius: 25) [16:48:34 -335823.208669] FAST spr round 4 (radius: 25) [16:50:10 -335807.863707] FAST spr round 5 (radius: 25) [16:51:44 -335796.012910] FAST spr round 6 (radius: 25) [16:53:15 -335791.294884] FAST spr round 7 (radius: 25) [16:54:47 -335791.294866] Model parameter optimization (eps = 1.000000) [16:54:52 -335791.159576] SLOW spr round 1 (radius: 5) [16:56:56 -335696.178068] SLOW spr round 2 (radius: 5) [16:58:55 -335686.064965] SLOW spr round 3 (radius: 5) [17:00:49 -335686.052330] SLOW spr round 4 (radius: 10) [17:02:49 -335685.649001] SLOW spr round 5 (radius: 5) [17:05:09 -335680.698898] SLOW spr round 6 (radius: 5) [17:07:13 -335680.698819] SLOW spr round 7 (radius: 10) [17:09:15 -335680.698809] SLOW spr round 8 (radius: 15) [17:12:31 -335680.328935] SLOW spr round 9 (radius: 5) [17:14:54 -335680.328933] SLOW spr round 10 (radius: 10) [17:17:09 -335680.328932] SLOW spr round 11 (radius: 15) [17:20:14 -335680.328932] SLOW spr round 12 (radius: 20) [17:25:12 -335680.328931] SLOW spr round 13 (radius: 25) [17:31:31 -335680.328931] Model parameter optimization (eps = 0.100000) [17:31:48] ML tree search #17, logLikelihood: -335471.591465 [17:31:48 -962416.929348] Initial branch length optimization [17:31:51 -807104.913578] Model parameter optimization (eps = 10.000000) [17:32:39 -805159.057680] AUTODETECT spr round 1 (radius: 5) [17:34:31 -638641.641288] AUTODETECT spr round 2 (radius: 10) [17:36:37 -489002.734589] AUTODETECT spr round 3 (radius: 15) [17:38:55 -425663.551138] AUTODETECT spr round 4 (radius: 20) [17:41:31 -384219.943020] AUTODETECT spr round 5 (radius: 25) [17:44:19 -374147.289557] SPR radius for FAST iterations: 25 (autodetect) [17:44:19 -374147.289557] Model parameter optimization (eps = 3.000000) [17:44:39 -373995.849261] FAST spr round 1 (radius: 25) [17:47:28 -336709.798704] FAST spr round 2 (radius: 25) [17:49:32 -335698.692371] FAST spr round 3 (radius: 25) [17:51:19 -335578.255797] FAST spr round 4 (radius: 25) [17:53:00 -335564.850832] FAST spr round 5 (radius: 25) [17:54:33 -335564.850567] Model parameter optimization (eps = 1.000000) [17:54:47 -335551.725675] SLOW spr round 1 (radius: 5) [17:56:59 -335480.191099] SLOW spr round 2 (radius: 5) [17:59:02 -335464.795207] SLOW spr round 3 (radius: 5) [18:01:00 -335459.825931] SLOW spr round 4 (radius: 5) [18:02:56 -335459.824520] SLOW spr round 5 (radius: 10) [18:04:55 -335458.338787] SLOW spr round 6 (radius: 5) [18:07:15 -335458.335690] SLOW spr round 7 (radius: 10) [18:09:26 -335458.298485] SLOW spr round 8 (radius: 15) [18:12:41 -335457.151927] SLOW spr round 9 (radius: 5) [18:15:04 -335457.146810] SLOW spr round 10 (radius: 10) [18:17:27 -335457.145815] SLOW spr round 11 (radius: 15) [18:20:45 -335457.145545] SLOW spr round 12 (radius: 20) [18:25:50 -335457.145435] SLOW spr round 13 (radius: 25) [18:32:06 -335457.145377] Model parameter optimization (eps = 0.100000) [18:32:11] ML tree search #18, logLikelihood: -335457.078311 [18:32:11 -965049.926282] Initial branch length optimization [18:32:14 -810848.172146] Model parameter optimization (eps = 10.000000) [18:32:52 -808941.233037] AUTODETECT spr round 1 (radius: 5) [18:34:45 -625790.137608] AUTODETECT spr round 2 (radius: 10) [18:36:49 -493940.473300] AUTODETECT spr round 3 (radius: 15) [18:39:12 -446874.756341] AUTODETECT spr round 4 (radius: 20) [18:42:19 -391234.503000] AUTODETECT spr round 5 (radius: 25) [18:45:19 -379987.568588] SPR radius for FAST iterations: 25 (autodetect) [18:45:19 -379987.568588] Model parameter optimization (eps = 3.000000) [18:45:36 -379824.802289] FAST spr round 1 (radius: 25) [18:48:19 -337927.596152] FAST spr round 2 (radius: 25) [18:50:26 -335635.036008] FAST spr round 3 (radius: 25) [18:52:15 -335556.127870] FAST spr round 4 (radius: 25) [18:53:54 -335542.786468] FAST spr round 5 (radius: 25) [18:55:26 -335542.783770] Model parameter optimization (eps = 1.000000) [18:55:40 -335534.385739] SLOW spr round 1 (radius: 5) [18:57:46 -335469.239214] SLOW spr round 2 (radius: 5) [18:59:45 -335462.313602] SLOW spr round 3 (radius: 5) [19:01:41 -335456.031834] SLOW spr round 4 (radius: 5) [19:03:38 -335450.007978] SLOW spr round 5 (radius: 5) [19:05:31 -335447.837927] SLOW spr round 6 (radius: 5) [19:07:23 -335447.837211] SLOW spr round 7 (radius: 10) [19:09:22 -335447.837078] SLOW spr round 8 (radius: 15) [19:12:49 -335447.837025] SLOW spr round 9 (radius: 20) [19:17:46 -335447.837000] SLOW spr round 10 (radius: 25) [19:24:12 -335447.836988] Model parameter optimization (eps = 0.100000) [19:24:19] ML tree search #19, logLikelihood: -335447.720080 [19:24:19 -969468.875010] Initial branch length optimization [19:24:22 -812773.035286] Model parameter optimization (eps = 10.000000) [19:24:57 -810992.335915] AUTODETECT spr round 1 (radius: 5) [19:26:49 -633011.510450] AUTODETECT spr round 2 (radius: 10) [19:29:01 -494256.542221] AUTODETECT spr round 3 (radius: 15) [19:31:24 -427572.609275] AUTODETECT spr round 4 (radius: 20) [19:33:56 -396155.740736] AUTODETECT spr round 5 (radius: 25) [19:37:04 -382600.965385] SPR radius for FAST iterations: 25 (autodetect) [19:37:04 -382600.965385] Model parameter optimization (eps = 3.000000) [19:37:10 -382597.328909] FAST spr round 1 (radius: 25) [19:39:50 -337525.770494] FAST spr round 2 (radius: 25) [19:41:53 -335980.806701] FAST spr round 3 (radius: 25) [19:43:42 -335773.885590] FAST spr round 4 (radius: 25) [19:45:18 -335758.673037] FAST spr round 5 (radius: 25) [19:46:48 -335758.673036] Model parameter optimization (eps = 1.000000) [19:47:04 -335593.007711] SLOW spr round 1 (radius: 5) [19:49:06 -335464.715505] SLOW spr round 2 (radius: 5) [19:51:09 -335454.246318] SLOW spr round 3 (radius: 5) [19:53:05 -335449.664999] SLOW spr round 4 (radius: 5) [19:54:59 -335448.384811] SLOW spr round 5 (radius: 5) [19:56:53 -335448.021015] SLOW spr round 6 (radius: 5) [19:58:49 -335448.020653] SLOW spr round 7 (radius: 10) [20:00:48 -335448.020581] SLOW spr round 8 (radius: 15) [20:04:17 -335446.889294] SLOW spr round 9 (radius: 5) [20:06:44 -335446.884033] SLOW spr round 10 (radius: 10) [20:09:02 -335446.883184] SLOW spr round 11 (radius: 15) [20:12:15 -335446.883050] SLOW spr round 12 (radius: 20) [20:17:17 -335446.883028] SLOW spr round 13 (radius: 25) [20:23:43 -335446.883025] Model parameter optimization (eps = 0.100000) [20:23:47] ML tree search #20, logLikelihood: -335446.854304 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.191603,0.311855) (0.233630,0.415887) (0.321376,1.025055) (0.253391,2.027126) 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: -335434.630793 AIC score: 674879.261586 / AICc score: 8718939.261586 / BIC score: 683602.787448 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=573). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 29 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IYD8/3_mltree/Q8IYD8.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IYD8/3_mltree/Q8IYD8.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IYD8/3_mltree/Q8IYD8.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IYD8/3_mltree/Q8IYD8.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IYD8/3_mltree/Q8IYD8.raxml.log Analysis started: 03-Jul-2021 11:55:25 / finished: 04-Jul-2021 08:19:13 Elapsed time: 73427.962 seconds Consumed energy: 7009.756 Wh (= 35 km in an electric car, or 175 km with an e-scooter!)