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 04-Jul-2021 14:58:39 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q2M3M2/2_msa/Q2M3M2_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q2M3M2/3_mltree/Q2M3M2 --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/Q2M3M2/2_msa/Q2M3M2_trimmed_msa.fasta [00:00:00] Loaded alignment with 875 taxa and 441 sites WARNING: Sequences tr_A0A2I2YI79_A0A2I2YI79_GORGO_9595 and tr_H2QB06_H2QB06_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YI79_A0A2I2YI79_GORGO_9595 and sp_P31639_SC5A2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2YI79_A0A2I2YI79_GORGO_9595 and tr_A0A2R9C6P9_A0A2R9C6P9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2ZN76_A0A2I2ZN76_GORGO_9595 and sp_P53794_SC5A3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2ZN76_A0A2I2ZN76_GORGO_9595 and tr_G7MMU9_G7MMU9_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I2ZN76_A0A2I2ZN76_GORGO_9595 and tr_G7P127_G7P127_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I2ZN76_A0A2I2ZN76_GORGO_9595 and tr_A0A2K6AVV5_A0A2K6AVV5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I2ZN76_A0A2I2ZN76_GORGO_9595 and tr_A0A2K5XDX0_A0A2K5XDX0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I2ZN76_A0A2I2ZN76_GORGO_9595 and tr_A0A2R8ZN24_A0A2R8ZN24_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QH08_G3QH08_GORGO_9595 and sp_Q8WWX8_SC5AB_HUMAN_9606 are exactly identical! WARNING: Sequences tr_B7NZM9_B7NZM9_RABIT_9986 and sp_P11170_SC5A1_RABIT_9986 are exactly identical! WARNING: Sequences sp_P31637_SC5A3_CANLF_9615 and tr_D2HCF2_D2HCF2_AILME_9646 are exactly identical! WARNING: Sequences sp_P31637_SC5A3_CANLF_9615 and tr_A0A2U3WCU8_A0A2U3WCU8_ODORO_9708 are exactly identical! WARNING: Sequences sp_P31637_SC5A3_CANLF_9615 and tr_A0A2U3YVP2_A0A2U3YVP2_LEPWE_9713 are exactly identical! WARNING: Sequences sp_P31637_SC5A3_CANLF_9615 and tr_A0A2Y9KJI8_A0A2Y9KJI8_ENHLU_391180 are exactly identical! WARNING: Sequences sp_P31637_SC5A3_CANLF_9615 and tr_A0A384D004_A0A384D004_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2I3RGZ4_A0A2I3RGZ4_PANTR_9598 and sp_A0PJK1_SC5AA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QLJ1_H2QLJ1_PANTR_9598 and tr_A0A2R9C7G1_A0A2R9C7G1_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R1F0_H2R1F0_PANTR_9598 and tr_A0A2R8ZK16_A0A2R8ZK16_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5QYK0_A0A1D5QYK0_MACMU_9544 and tr_A0A2K6DTT8_A0A2K6DTT8_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6REJ5_F6REJ5_MACMU_9544 and tr_G7Q108_G7Q108_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6REJ5_F6REJ5_MACMU_9544 and tr_A0A096NHZ7_A0A096NHZ7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6REJ5_F6REJ5_MACMU_9544 and tr_A0A2K5NFQ2_A0A2K5NFQ2_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6REJ5_F6REJ5_MACMU_9544 and tr_A0A2K6AQJ7_A0A2K6AQJ7_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6T0X3_F6T0X3_MACMU_9544 and tr_G7NVM9_G7NVM9_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GMX1_F7GMX1_MACMU_9544 and tr_G7PF95_G7PF95_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GMX1_F7GMX1_MACMU_9544 and tr_A0A2K6DNL8_A0A2K6DNL8_MACNE_9545 are exactly identical! WARNING: Sequences tr_F1SB19_F1SB19_PIG_9823 and sp_Q5FY69_SC5AA_PIG_9823 are exactly identical! WARNING: Sequences tr_G7Q0R6_G7Q0R6_MACFA_9541 and tr_A0A2K6BC45_A0A2K6BC45_MACNE_9545 are exactly identical! WARNING: Sequences tr_W2QXH2_W2QXH2_PHYPN_761204 and tr_A0A0W8DYM2_A0A0W8DYM2_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2QXH2_W2QXH2_PHYPN_761204 and tr_W2FUR7_W2FUR7_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A096NJN9_A0A096NJN9_PAPAN_9555 and tr_A0A2K5NUS9_A0A2K5NUS9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NJN9_A0A096NJN9_PAPAN_9555 and tr_A0A2K5YKU4_A0A2K5YKU4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A087R944_A0A087R944_APTFO_9233 and tr_A0A0A0A327_A0A0A0A327_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A226MY72_A0A226MY72_CALSU_9009 and tr_A0A226PHT3_A0A226PHT3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NMK1_A0A226NMK1_CALSU_9009 and tr_A0A226NYH4_A0A226NYH4_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2K5KJ56_A0A2K5KJ56_CERAT_9531 and tr_A0A2K5YWG4_A0A2K5YWG4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5M8H9_A0A2K5M8H9_CERAT_9531 and tr_A0A2K5XUS3_A0A2K5XUS3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4ABL3_A0A2U4ABL3_TURTR_9739 and tr_A0A2Y9LGH6_A0A2Y9LGH6_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4ABL3_A0A2U4ABL3_TURTR_9739 and tr_A0A2Y9SC12_A0A2Y9SC12_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4ABL3_A0A2U4ABL3_TURTR_9739 and tr_A0A384A8Y2_A0A384A8Y2_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 41 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/Q2M3M2/3_mltree/Q2M3M2.raxml.reduced.phy Alignment comprises 1 partitions and 441 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 441 / 441 Gaps: 10.47 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q2M3M2/3_mltree/Q2M3M2.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 875 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 63 / 5040 [00:00:00] Data distribution: max. searches per worker: 20 Starting ML tree search with 20 distinct starting trees [00:00:00 -450852.999315] Initial branch length optimization [00:00:03 -386952.027027] Model parameter optimization (eps = 10.000000) [00:00:25 -385119.582937] AUTODETECT spr round 1 (radius: 5) [00:01:44 -264606.939799] AUTODETECT spr round 2 (radius: 10) [00:02:55 -198190.751102] AUTODETECT spr round 3 (radius: 15) [00:04:22 -170340.184287] AUTODETECT spr round 4 (radius: 20) [00:06:00 -166796.114555] AUTODETECT spr round 5 (radius: 25) [00:08:10 -166271.708882] SPR radius for FAST iterations: 25 (autodetect) [00:08:10 -166271.708882] Model parameter optimization (eps = 3.000000) [00:08:26 -166175.703115] FAST spr round 1 (radius: 25) [00:10:02 -150436.927635] FAST spr round 2 (radius: 25) [00:11:17 -149873.440388] FAST spr round 3 (radius: 25) [00:12:32 -149827.502820] FAST spr round 4 (radius: 25) [00:13:51 -149827.502157] Model parameter optimization (eps = 1.000000) [00:14:09 -149809.366947] SLOW spr round 1 (radius: 5) [00:16:37 -149776.873315] SLOW spr round 2 (radius: 5) [00:19:01 -149772.845895] SLOW spr round 3 (radius: 5) [00:21:14 -149768.498986] SLOW spr round 4 (radius: 5) [00:23:28 -149768.496035] SLOW spr round 5 (radius: 10) [00:25:40 -149766.321958] SLOW spr round 6 (radius: 5) [00:28:25 -149766.321834] SLOW spr round 7 (radius: 10) [00:30:45 -149766.321816] SLOW spr round 8 (radius: 15) [00:34:01 -149766.087054] SLOW spr round 9 (radius: 5) [00:36:39 -149766.086984] SLOW spr round 10 (radius: 10) [00:39:04 -149766.086980] SLOW spr round 11 (radius: 15) [00:42:24 -149766.086978] SLOW spr round 12 (radius: 20) [00:47:20 -149766.086977] SLOW spr round 13 (radius: 25) [00:53:52 -149766.086976] Model parameter optimization (eps = 0.100000) [00:53:58] ML tree search #1, logLikelihood: -149766.029649 [00:53:58 -452392.802941] Initial branch length optimization [00:54:02 -388800.335653] Model parameter optimization (eps = 10.000000) [00:54:39 -386941.047243] AUTODETECT spr round 1 (radius: 5) [00:56:48 -264688.605720] AUTODETECT spr round 2 (radius: 10) [00:59:10 -192875.513347] AUTODETECT spr round 3 (radius: 15) [01:01:44 -167462.099419] AUTODETECT spr round 4 (radius: 20) [01:04:54 -163990.906539] AUTODETECT spr round 5 (radius: 25) [01:08:35 -163451.151682] SPR radius for FAST iterations: 25 (autodetect) [01:08:35 -163451.151682] Model parameter optimization (eps = 3.000000) [01:09:05 -163337.274647] FAST spr round 1 (radius: 25) [01:11:49 -150284.285010] FAST spr round 2 (radius: 25) [01:13:56 -149855.091531] FAST spr round 3 (radius: 25) [01:15:54 -149824.044142] FAST spr round 4 (radius: 25) [01:17:45 -149819.477146] FAST spr round 5 (radius: 25) [01:19:32 -149819.476224] Model parameter optimization (eps = 1.000000) [01:19:53 -149812.139445] SLOW spr round 1 (radius: 5) [01:22:16 -149781.096170] SLOW spr round 2 (radius: 5) [01:24:24 -149777.576274] SLOW spr round 3 (radius: 5) [01:26:29 -149777.575226] SLOW spr round 4 (radius: 10) [01:28:38 -149772.654531] SLOW spr round 5 (radius: 5) [01:31:10 -149769.664123] SLOW spr round 6 (radius: 5) [01:33:31 -149769.663202] SLOW spr round 7 (radius: 10) [01:35:52 -149769.594315] SLOW spr round 8 (radius: 15) [01:39:32 -149769.406108] SLOW spr round 9 (radius: 5) [01:42:21 -149769.406008] SLOW spr round 10 (radius: 10) [01:44:55 -149769.406004] SLOW spr round 11 (radius: 15) [01:48:22 -149769.406003] SLOW spr round 12 (radius: 20) [01:53:35 -149769.171182] SLOW spr round 13 (radius: 5) [01:56:22 -149769.171082] SLOW spr round 14 (radius: 10) [01:59:03 -149769.171081] SLOW spr round 15 (radius: 15) [02:02:26 -149769.171080] SLOW spr round 16 (radius: 20) [02:07:34 -149769.171079] SLOW spr round 17 (radius: 25) [02:14:10 -149769.171079] Model parameter optimization (eps = 0.100000) [02:14:19] ML tree search #2, logLikelihood: -149769.130048 [02:14:19 -451523.795861] Initial branch length optimization [02:14:21 -387672.895050] Model parameter optimization (eps = 10.000000) [02:14:57 -385864.400800] AUTODETECT spr round 1 (radius: 5) [02:17:04 -270528.845478] AUTODETECT spr round 2 (radius: 10) [02:19:22 -208913.729872] AUTODETECT spr round 3 (radius: 15) [02:22:02 -175812.368050] AUTODETECT spr round 4 (radius: 20) [02:25:25 -169754.711284] AUTODETECT spr round 5 (radius: 25) [02:29:09 -168495.464163] SPR radius for FAST iterations: 25 (autodetect) [02:29:09 -168495.464163] Model parameter optimization (eps = 3.000000) [02:29:32 -168376.360627] FAST spr round 1 (radius: 25) [02:32:14 -150510.222907] FAST spr round 2 (radius: 25) [02:34:26 -149893.171451] FAST spr round 3 (radius: 25) [02:36:27 -149834.609907] FAST spr round 4 (radius: 25) [02:38:21 -149827.975734] FAST spr round 5 (radius: 25) [02:40:06 -149827.503913] FAST spr round 6 (radius: 25) [02:41:44 -149827.503031] Model parameter optimization (eps = 1.000000) [02:42:06 -149817.650129] SLOW spr round 1 (radius: 5) [02:44:13 -149794.112385] SLOW spr round 2 (radius: 5) [02:46:19 -149793.286098] SLOW spr round 3 (radius: 5) [02:48:23 -149788.452370] SLOW spr round 4 (radius: 5) [02:50:30 -149788.451829] SLOW spr round 5 (radius: 10) [02:52:44 -149783.699408] SLOW spr round 6 (radius: 5) [02:55:30 -149781.346860] SLOW spr round 7 (radius: 5) [02:57:50 -149779.772989] SLOW spr round 8 (radius: 5) [03:00:01 -149779.602752] SLOW spr round 9 (radius: 5) [03:02:11 -149779.602746] SLOW spr round 10 (radius: 10) [03:04:28 -149770.847098] SLOW spr round 11 (radius: 5) [03:07:03 -149769.311074] SLOW spr round 12 (radius: 5) [03:09:19 -149764.921243] SLOW spr round 13 (radius: 5) [03:11:27 -149764.412469] SLOW spr round 14 (radius: 5) [03:13:37 -149764.411961] SLOW spr round 15 (radius: 10) [03:15:44 -149764.411940] SLOW spr round 16 (radius: 15) [03:19:30 -149764.411939] SLOW spr round 17 (radius: 20) [03:24:11 -149764.411938] SLOW spr round 18 (radius: 25) [03:30:43 -149764.411938] Model parameter optimization (eps = 0.100000) [03:30:53] ML tree search #3, logLikelihood: -149764.253852 [03:30:53 -454174.020005] Initial branch length optimization [03:30:55 -390483.056049] Model parameter optimization (eps = 10.000000) [03:31:25 -388559.199517] AUTODETECT spr round 1 (radius: 5) [03:33:40 -268450.322605] AUTODETECT spr round 2 (radius: 10) [03:36:02 -203766.582608] AUTODETECT spr round 3 (radius: 15) [03:38:35 -173114.980329] AUTODETECT spr round 4 (radius: 20) [03:41:42 -168079.144040] AUTODETECT spr round 5 (radius: 25) [03:45:37 -167048.153865] SPR radius for FAST iterations: 25 (autodetect) [03:45:37 -167048.153865] Model parameter optimization (eps = 3.000000) [03:46:06 -166929.452984] FAST spr round 1 (radius: 25) [03:48:56 -150661.300905] FAST spr round 2 (radius: 25) [03:51:15 -149859.710070] FAST spr round 3 (radius: 25) [03:53:18 -149836.601798] FAST spr round 4 (radius: 25) [03:55:11 -149833.268621] FAST spr round 5 (radius: 25) [03:57:04 -149829.745905] FAST spr round 6 (radius: 25) [03:58:43 -149829.383433] FAST spr round 7 (radius: 25) [04:00:22 -149829.383336] Model parameter optimization (eps = 1.000000) [04:00:40 -149818.998777] SLOW spr round 1 (radius: 5) [04:02:46 -149795.588488] SLOW spr round 2 (radius: 5) [04:04:54 -149792.875585] SLOW spr round 3 (radius: 5) [04:07:00 -149792.389607] SLOW spr round 4 (radius: 5) [04:09:05 -149792.388728] SLOW spr round 5 (radius: 10) [04:11:23 -149791.616602] SLOW spr round 6 (radius: 5) [04:14:09 -149790.767832] SLOW spr round 7 (radius: 5) [04:16:31 -149790.767780] SLOW spr round 8 (radius: 10) [04:18:49 -149790.767776] SLOW spr round 9 (radius: 15) [04:22:36 -149789.430967] SLOW spr round 10 (radius: 5) [04:25:15 -149789.430553] SLOW spr round 11 (radius: 10) [04:27:39 -149789.430525] SLOW spr round 12 (radius: 15) [04:31:05 -149789.016413] SLOW spr round 13 (radius: 5) [04:33:55 -149789.014930] SLOW spr round 14 (radius: 10) [04:36:28 -149789.014905] SLOW spr round 15 (radius: 15) [04:39:45 -149789.014903] SLOW spr round 16 (radius: 20) [04:44:59 -149788.780495] SLOW spr round 17 (radius: 5) [04:47:34 -149788.780305] SLOW spr round 18 (radius: 10) [04:50:10 -149788.780305] SLOW spr round 19 (radius: 15) [04:53:29 -149788.780304] SLOW spr round 20 (radius: 20) [04:59:00 -149788.780303] SLOW spr round 21 (radius: 25) [05:05:27 -149788.780303] Model parameter optimization (eps = 0.100000) [05:05:36] ML tree search #4, logLikelihood: -149788.670144 [05:05:36 -448186.216712] Initial branch length optimization [05:05:39 -384576.499169] Model parameter optimization (eps = 10.000000) [05:06:24 -382741.872485] AUTODETECT spr round 1 (radius: 5) [05:08:20 -271569.468283] AUTODETECT spr round 2 (radius: 10) [05:10:27 -205363.532584] AUTODETECT spr round 3 (radius: 15) [05:13:00 -176266.381858] AUTODETECT spr round 4 (radius: 20) [05:16:02 -168644.918955] AUTODETECT spr round 5 (radius: 25) [05:19:54 -168132.413623] SPR radius for FAST iterations: 25 (autodetect) [05:19:54 -168132.413623] Model parameter optimization (eps = 3.000000) [05:20:19 -168005.588764] FAST spr round 1 (radius: 25) [05:23:07 -150366.245377] FAST spr round 2 (radius: 25) [05:25:23 -149891.254704] FAST spr round 3 (radius: 25) [05:27:21 -149856.466321] FAST spr round 4 (radius: 25) [05:29:14 -149852.986896] FAST spr round 5 (radius: 25) [05:30:59 -149852.985423] Model parameter optimization (eps = 1.000000) [05:31:23 -149848.115021] SLOW spr round 1 (radius: 5) [05:33:39 -149791.748688] SLOW spr round 2 (radius: 5) [05:36:00 -149786.821258] SLOW spr round 3 (radius: 5) [05:38:05 -149786.818169] SLOW spr round 4 (radius: 10) [05:40:18 -149785.395225] SLOW spr round 5 (radius: 5) [05:42:49 -149785.394904] SLOW spr round 6 (radius: 10) [05:45:05 -149784.709766] SLOW spr round 7 (radius: 5) [05:47:30 -149784.709465] SLOW spr round 8 (radius: 10) [05:49:55 -149784.709445] SLOW spr round 9 (radius: 15) [05:53:18 -149784.709440] SLOW spr round 10 (radius: 20) [05:58:28 -149784.709438] SLOW spr round 11 (radius: 25) [06:05:04 -149784.709436] Model parameter optimization (eps = 0.100000) [06:05:26] ML tree search #5, logLikelihood: -149783.443547 [06:05:26 -452067.996365] Initial branch length optimization [06:05:29 -387598.222802] Model parameter optimization (eps = 10.000000) [06:06:03 -385712.446772] AUTODETECT spr round 1 (radius: 5) [06:07:59 -273837.886652] AUTODETECT spr round 2 (radius: 10) [06:10:28 -204073.947602] AUTODETECT spr round 3 (radius: 15) [06:12:53 -179886.565893] AUTODETECT spr round 4 (radius: 20) [06:15:45 -169673.019497] AUTODETECT spr round 5 (radius: 25) [06:18:54 -166829.670369] SPR radius for FAST iterations: 25 (autodetect) [06:18:54 -166829.670369] Model parameter optimization (eps = 3.000000) [06:19:21 -166681.702159] FAST spr round 1 (radius: 25) [06:22:13 -150624.804852] FAST spr round 2 (radius: 25) [06:24:20 -149930.874912] FAST spr round 3 (radius: 25) [06:26:14 -149848.580003] FAST spr round 4 (radius: 25) [06:28:08 -149823.163705] FAST spr round 5 (radius: 25) [06:30:02 -149810.886667] FAST spr round 6 (radius: 25) [06:31:48 -149810.874209] Model parameter optimization (eps = 1.000000) [06:32:08 -149801.689978] SLOW spr round 1 (radius: 5) [06:34:28 -149768.385166] SLOW spr round 2 (radius: 5) [06:36:34 -149762.181126] SLOW spr round 3 (radius: 5) [06:38:36 -149761.656701] SLOW spr round 4 (radius: 5) [06:40:38 -149761.656223] SLOW spr round 5 (radius: 10) [06:42:42 -149757.022159] SLOW spr round 6 (radius: 5) [06:45:10 -149757.021578] SLOW spr round 7 (radius: 10) [06:47:26 -149757.021065] SLOW spr round 8 (radius: 15) [06:51:01 -149757.020545] SLOW spr round 9 (radius: 20) [06:56:19 -149757.020013] SLOW spr round 10 (radius: 25) [07:02:50 -149756.853247] SLOW spr round 11 (radius: 5) [07:05:27 -149756.852649] SLOW spr round 12 (radius: 10) [07:07:54 -149756.852082] SLOW spr round 13 (radius: 15) [07:11:08 -149756.851504] SLOW spr round 14 (radius: 20) [07:16:35 -149756.850913] SLOW spr round 15 (radius: 25) [07:22:57 -149756.850309] Model parameter optimization (eps = 0.100000) [07:23:02] ML tree search #6, logLikelihood: -149756.776699 [07:23:02 -451686.036364] Initial branch length optimization [07:23:05 -388409.526940] Model parameter optimization (eps = 10.000000) [07:23:42 -386545.775882] AUTODETECT spr round 1 (radius: 5) [07:25:34 -270803.870532] AUTODETECT spr round 2 (radius: 10) [07:27:46 -210080.132946] AUTODETECT spr round 3 (radius: 15) [07:30:18 -179486.793003] AUTODETECT spr round 4 (radius: 20) [07:33:38 -168623.700117] AUTODETECT spr round 5 (radius: 25) [07:37:05 -166934.822595] SPR radius for FAST iterations: 25 (autodetect) [07:37:05 -166934.822595] Model parameter optimization (eps = 3.000000) [07:37:33 -166715.297351] FAST spr round 1 (radius: 25) [07:40:19 -150340.747209] FAST spr round 2 (radius: 25) [07:42:36 -149891.876227] FAST spr round 3 (radius: 25) [07:44:27 -149857.274410] FAST spr round 4 (radius: 25) [07:46:09 -149853.769898] FAST spr round 5 (radius: 25) [07:47:46 -149853.769254] Model parameter optimization (eps = 1.000000) [07:48:05 -149846.359384] SLOW spr round 1 (radius: 5) [07:50:15 -149797.378079] SLOW spr round 2 (radius: 5) [07:52:26 -149785.124484] SLOW spr round 3 (radius: 5) [07:54:29 -149784.913725] SLOW spr round 4 (radius: 5) [07:56:32 -149784.912463] SLOW spr round 5 (radius: 10) [07:58:37 -149784.520320] SLOW spr round 6 (radius: 5) [08:01:05 -149783.969626] SLOW spr round 7 (radius: 5) [08:03:19 -149783.968445] SLOW spr round 8 (radius: 10) [08:05:27 -149783.967803] SLOW spr round 9 (radius: 15) [08:08:51 -149782.984657] SLOW spr round 10 (radius: 5) [08:11:29 -149782.984255] SLOW spr round 11 (radius: 10) [08:13:58 -149782.983891] SLOW spr round 12 (radius: 15) [08:17:12 -149782.983522] SLOW spr round 13 (radius: 20) [08:22:24 -149782.983147] SLOW spr round 14 (radius: 25) [08:28:51 -149782.982765] Model parameter optimization (eps = 0.100000) [08:28:59] ML tree search #7, logLikelihood: -149782.960192 [08:29:00 -451990.377560] Initial branch length optimization [08:29:02 -386469.237337] Model parameter optimization (eps = 10.000000) [08:29:34 -384776.525425] AUTODETECT spr round 1 (radius: 5) [08:31:30 -270094.359774] AUTODETECT spr round 2 (radius: 10) [08:33:48 -197133.101378] AUTODETECT spr round 3 (radius: 15) [08:36:14 -173827.953671] AUTODETECT spr round 4 (radius: 20) [08:39:02 -166143.304032] AUTODETECT spr round 5 (radius: 25) [08:42:06 -164191.061117] SPR radius for FAST iterations: 25 (autodetect) [08:42:06 -164191.061117] Model parameter optimization (eps = 3.000000) [08:42:29 -164064.684767] FAST spr round 1 (radius: 25) [08:45:04 -150661.078258] FAST spr round 2 (radius: 25) [08:47:14 -149925.092889] FAST spr round 3 (radius: 25) [08:49:10 -149856.570947] FAST spr round 4 (radius: 25) [08:50:55 -149821.818433] FAST spr round 5 (radius: 25) [08:52:34 -149817.817962] FAST spr round 6 (radius: 25) [08:54:15 -149817.817782] Model parameter optimization (eps = 1.000000) [08:54:35 -149811.579053] SLOW spr round 1 (radius: 5) [08:56:47 -149783.829420] SLOW spr round 2 (radius: 5) [08:58:54 -149783.816747] SLOW spr round 3 (radius: 10) [09:01:05 -149780.970521] SLOW spr round 4 (radius: 5) [09:03:42 -149778.282840] SLOW spr round 5 (radius: 5) [09:05:57 -149778.280995] SLOW spr round 6 (radius: 10) [09:08:07 -149778.280714] SLOW spr round 7 (radius: 15) [09:11:25 -149777.804574] SLOW spr round 8 (radius: 5) [09:13:59 -149777.804468] SLOW spr round 9 (radius: 10) [09:16:21 -149777.804438] SLOW spr round 10 (radius: 15) [09:19:48 -149777.804427] SLOW spr round 11 (radius: 20) [09:24:41 -149777.804422] SLOW spr round 12 (radius: 25) [09:31:00 -149777.751767] Model parameter optimization (eps = 0.100000) [09:31:11] ML tree search #8, logLikelihood: -149777.563934 [09:31:11 -452110.692892] Initial branch length optimization [09:31:14 -388217.696494] Model parameter optimization (eps = 10.000000) [09:31:57 -386350.995725] AUTODETECT spr round 1 (radius: 5) [09:34:04 -268758.269024] AUTODETECT spr round 2 (radius: 10) [09:36:26 -199647.208135] AUTODETECT spr round 3 (radius: 15) [09:38:46 -174538.266550] AUTODETECT spr round 4 (radius: 20) [09:41:53 -166150.740105] AUTODETECT spr round 5 (radius: 25) [09:45:23 -165417.671409] SPR radius for FAST iterations: 25 (autodetect) [09:45:23 -165417.671409] Model parameter optimization (eps = 3.000000) [09:45:50 -165287.717347] FAST spr round 1 (radius: 25) [09:48:34 -151110.938326] FAST spr round 2 (radius: 25) [09:50:43 -150112.793839] FAST spr round 3 (radius: 25) [09:52:42 -149888.170079] FAST spr round 4 (radius: 25) [09:54:30 -149874.997108] FAST spr round 5 (radius: 25) [09:56:09 -149873.593089] FAST spr round 6 (radius: 25) [09:57:49 -149873.591159] Model parameter optimization (eps = 1.000000) [09:58:09 -149862.435322] SLOW spr round 1 (radius: 5) [10:00:19 -149796.681102] SLOW spr round 2 (radius: 5) [10:02:23 -149790.869454] SLOW spr round 3 (radius: 5) [10:04:24 -149790.865823] SLOW spr round 4 (radius: 10) [10:06:28 -149781.957794] SLOW spr round 5 (radius: 5) [10:08:56 -149779.399040] SLOW spr round 6 (radius: 5) [10:11:08 -149779.398060] SLOW spr round 7 (radius: 10) [10:13:17 -149775.756816] SLOW spr round 8 (radius: 5) [10:15:52 -149775.756803] SLOW spr round 9 (radius: 10) [10:18:14 -149774.586101] SLOW spr round 10 (radius: 5) [10:20:49 -149774.585794] SLOW spr round 11 (radius: 10) [10:23:15 -149774.585792] SLOW spr round 12 (radius: 15) [10:27:00 -149774.585792] SLOW spr round 13 (radius: 20) [10:32:21 -149774.585791] SLOW spr round 14 (radius: 25) [10:39:22 -149774.585791] Model parameter optimization (eps = 0.100000) [10:39:32] ML tree search #9, logLikelihood: -149774.372228 [10:39:33 -451672.490073] Initial branch length optimization [10:39:36 -387766.455287] Model parameter optimization (eps = 10.000000) [10:40:11 -385881.084838] AUTODETECT spr round 1 (radius: 5) [10:41:15 -263085.210826] AUTODETECT spr round 2 (radius: 10) [10:42:32 -202376.098850] AUTODETECT spr round 3 (radius: 15) [10:43:57 -178251.835555] AUTODETECT spr round 4 (radius: 20) [10:45:49 -169495.749199] AUTODETECT spr round 5 (radius: 25) [10:47:45 -168904.448847] SPR radius for FAST iterations: 25 (autodetect) [10:47:45 -168904.448847] Model parameter optimization (eps = 3.000000) [10:48:04 -168761.747355] FAST spr round 1 (radius: 25) [10:49:36 -150524.815361] FAST spr round 2 (radius: 25) [10:50:51 -149920.349836] FAST spr round 3 (radius: 25) [10:52:04 -149848.550049] FAST spr round 4 (radius: 25) [10:53:01 -149821.488387] FAST spr round 5 (radius: 25) [10:54:20 -149821.486828] Model parameter optimization (eps = 1.000000) [10:54:38 -149809.655733] SLOW spr round 1 (radius: 5) [10:56:22 -149771.443363] SLOW spr round 2 (radius: 5) [10:57:51 -149768.941553] SLOW spr round 3 (radius: 5) [10:59:10 -149768.884899] SLOW spr round 4 (radius: 10) [11:01:31 -149765.907873] SLOW spr round 5 (radius: 5) [11:04:25 -149760.805193] SLOW spr round 6 (radius: 5) [11:06:56 -149760.804950] SLOW spr round 7 (radius: 10) [11:09:10 -149759.624386] SLOW spr round 8 (radius: 5) [11:11:42 -149759.624136] SLOW spr round 9 (radius: 10) [11:14:04 -149759.624128] SLOW spr round 10 (radius: 15) [11:17:31 -149759.396307] SLOW spr round 11 (radius: 5) [11:20:08 -149759.396061] SLOW spr round 12 (radius: 10) [11:22:28 -149759.396054] SLOW spr round 13 (radius: 15) [11:25:39 -149759.396053] SLOW spr round 14 (radius: 20) [11:30:38 -149759.396052] SLOW spr round 15 (radius: 25) [11:37:15 -149759.241901] SLOW spr round 16 (radius: 5) [11:39:55 -149759.241853] SLOW spr round 17 (radius: 10) [11:42:25 -149759.241852] SLOW spr round 18 (radius: 15) [11:45:40 -149759.241851] SLOW spr round 19 (radius: 20) [11:50:40 -149759.241850] SLOW spr round 20 (radius: 25) [11:57:15 -149759.241849] Model parameter optimization (eps = 0.100000) [11:57:24] ML tree search #10, logLikelihood: -149759.134626 [11:57:24 -452256.649578] Initial branch length optimization [11:57:27 -388475.386596] Model parameter optimization (eps = 10.000000) [11:58:09 -386694.568016] AUTODETECT spr round 1 (radius: 5) [12:00:08 -269137.183765] AUTODETECT spr round 2 (radius: 10) [12:02:14 -207336.448000] AUTODETECT spr round 3 (radius: 15) [12:04:31 -175679.977187] AUTODETECT spr round 4 (radius: 20) [12:07:37 -167466.425505] AUTODETECT spr round 5 (radius: 25) [12:11:04 -165898.920034] SPR radius for FAST iterations: 25 (autodetect) [12:11:04 -165898.920034] Model parameter optimization (eps = 3.000000) [12:11:28 -165748.669241] FAST spr round 1 (radius: 25) [12:14:09 -150726.530267] FAST spr round 2 (radius: 25) [12:16:23 -149857.192300] FAST spr round 3 (radius: 25) [12:18:18 -149827.206654] FAST spr round 4 (radius: 25) [12:20:03 -149826.041422] FAST spr round 5 (radius: 25) [12:21:45 -149826.041363] Model parameter optimization (eps = 1.000000) [12:22:05 -149820.912899] SLOW spr round 1 (radius: 5) [12:24:15 -149794.120446] SLOW spr round 2 (radius: 5) [12:26:24 -149787.056453] SLOW spr round 3 (radius: 5) [12:28:27 -149783.927133] SLOW spr round 4 (radius: 5) [12:30:28 -149783.691737] SLOW spr round 5 (radius: 5) [12:32:29 -149783.482652] SLOW spr round 6 (radius: 5) [12:34:30 -149783.481921] SLOW spr round 7 (radius: 10) [12:36:43 -149776.187948] SLOW spr round 8 (radius: 5) [12:39:22 -149776.187443] SLOW spr round 9 (radius: 10) [12:41:49 -149776.187221] SLOW spr round 10 (radius: 15) [12:45:05 -149776.187083] SLOW spr round 11 (radius: 20) [12:50:33 -149776.186994] SLOW spr round 12 (radius: 25) [12:57:47 -149776.186937] Model parameter optimization (eps = 0.100000) [12:57:57] ML tree search #11, logLikelihood: -149776.041889 [12:57:57 -451746.203602] Initial branch length optimization [12:58:00 -387161.975749] Model parameter optimization (eps = 10.000000) [12:58:38 -385337.767712] AUTODETECT spr round 1 (radius: 5) [13:00:34 -270747.624019] AUTODETECT spr round 2 (radius: 10) [13:02:50 -197562.504263] AUTODETECT spr round 3 (radius: 15) [13:05:21 -170625.907717] AUTODETECT spr round 4 (radius: 20) [13:08:44 -165999.014361] AUTODETECT spr round 5 (radius: 25) [13:12:41 -165634.705423] SPR radius for FAST iterations: 25 (autodetect) [13:12:41 -165634.705423] Model parameter optimization (eps = 3.000000) [13:13:09 -165474.866907] FAST spr round 1 (radius: 25) [13:15:56 -150296.259779] FAST spr round 2 (radius: 25) [13:18:14 -149886.603492] FAST spr round 3 (radius: 25) [13:20:17 -149840.032838] FAST spr round 4 (radius: 25) [13:22:12 -149836.159083] FAST spr round 5 (radius: 25) [13:23:59 -149835.124538] FAST spr round 6 (radius: 25) [13:25:34 -149835.122288] Model parameter optimization (eps = 1.000000) [13:25:56 -149826.122741] SLOW spr round 1 (radius: 5) [13:28:02 -149781.668988] SLOW spr round 2 (radius: 5) [13:30:09 -149769.317561] SLOW spr round 3 (radius: 5) [13:32:13 -149768.203885] SLOW spr round 4 (radius: 5) [13:34:13 -149768.202305] SLOW spr round 5 (radius: 10) [13:36:20 -149764.473290] SLOW spr round 6 (radius: 5) [13:39:07 -149763.713285] SLOW spr round 7 (radius: 5) [13:41:24 -149763.712720] SLOW spr round 8 (radius: 10) [13:43:35 -149763.590495] SLOW spr round 9 (radius: 5) [13:46:13 -149763.589542] SLOW spr round 10 (radius: 10) [13:48:37 -149763.588954] SLOW spr round 11 (radius: 15) [13:51:57 -149763.588377] SLOW spr round 12 (radius: 20) [13:57:05 -149763.355574] SLOW spr round 13 (radius: 5) [13:59:41 -149763.354854] SLOW spr round 14 (radius: 10) [14:02:08 -149763.354242] SLOW spr round 15 (radius: 15) [14:05:22 -149763.353617] SLOW spr round 16 (radius: 20) [14:10:27 -149763.352979] SLOW spr round 17 (radius: 25) [14:17:09 -149763.190789] SLOW spr round 18 (radius: 5) [14:20:04 -149763.190079] SLOW spr round 19 (radius: 10) [14:22:38 -149763.189399] SLOW spr round 20 (radius: 15) [14:25:55 -149763.188704] SLOW spr round 21 (radius: 20) [14:31:05 -149763.187995] SLOW spr round 22 (radius: 25) [14:37:41 -149763.187271] Model parameter optimization (eps = 0.100000) [14:37:53] ML tree search #12, logLikelihood: -149763.041291 [14:37:53 -451140.746857] Initial branch length optimization [14:37:56 -386535.226611] Model parameter optimization (eps = 10.000000) [14:38:29 -384747.705507] AUTODETECT spr round 1 (radius: 5) [14:40:30 -271536.365174] AUTODETECT spr round 2 (radius: 10) [14:42:40 -200562.132800] AUTODETECT spr round 3 (radius: 15) [14:45:02 -174458.247241] AUTODETECT spr round 4 (radius: 20) [14:47:57 -166624.819104] AUTODETECT spr round 5 (radius: 25) [14:51:30 -165147.869047] SPR radius for FAST iterations: 25 (autodetect) [14:51:30 -165147.869047] Model parameter optimization (eps = 3.000000) [14:51:52 -165010.015672] FAST spr round 1 (radius: 25) [14:54:32 -150378.632621] FAST spr round 2 (radius: 25) [14:56:38 -149940.391297] FAST spr round 3 (radius: 25) [14:58:43 -149860.174507] FAST spr round 4 (radius: 25) [15:00:38 -149831.855617] FAST spr round 5 (radius: 25) [15:02:20 -149825.595861] FAST spr round 6 (radius: 25) [15:03:58 -149825.595852] Model parameter optimization (eps = 1.000000) [15:04:22 -149816.544879] SLOW spr round 1 (radius: 5) [15:06:34 -149773.649881] SLOW spr round 2 (radius: 5) [15:08:42 -149770.052453] SLOW spr round 3 (radius: 5) [15:10:59 -149770.051344] SLOW spr round 4 (radius: 10) [15:13:04 -149767.925797] SLOW spr round 5 (radius: 5) [15:15:33 -149767.858666] SLOW spr round 6 (radius: 10) [15:17:49 -149766.813455] SLOW spr round 7 (radius: 5) [15:20:17 -149766.813407] SLOW spr round 8 (radius: 10) [15:22:42 -149766.813407] SLOW spr round 9 (radius: 15) [15:26:01 -149765.817341] SLOW spr round 10 (radius: 5) [15:28:34 -149765.817308] SLOW spr round 11 (radius: 10) [15:30:56 -149765.817308] SLOW spr round 12 (radius: 15) [15:34:06 -149765.817308] SLOW spr round 13 (radius: 20) [15:39:15 -149765.817308] SLOW spr round 14 (radius: 25) [15:46:11 -149762.593542] SLOW spr round 15 (radius: 5) [15:48:52 -149762.592576] SLOW spr round 16 (radius: 10) [15:51:25 -149762.592514] SLOW spr round 17 (radius: 15) [15:54:37 -149762.356723] SLOW spr round 18 (radius: 5) [15:57:16 -149762.356665] SLOW spr round 19 (radius: 10) [15:59:47 -149762.356665] SLOW spr round 20 (radius: 15) [16:03:13 -149762.356665] SLOW spr round 21 (radius: 20) [16:08:22 -149762.356665] SLOW spr round 22 (radius: 25) [16:14:43 -149762.356665] Model parameter optimization (eps = 0.100000) [16:14:54] ML tree search #13, logLikelihood: -149762.204368 [16:14:54 -450437.718942] Initial branch length optimization [16:14:57 -386748.176267] Model parameter optimization (eps = 10.000000) [16:15:37 -385049.986025] AUTODETECT spr round 1 (radius: 5) [16:17:35 -271417.657957] AUTODETECT spr round 2 (radius: 10) [16:20:03 -202468.120128] AUTODETECT spr round 3 (radius: 15) [16:22:41 -170258.641341] AUTODETECT spr round 4 (radius: 20) [16:26:14 -164061.811888] AUTODETECT spr round 5 (radius: 25) [16:30:25 -163558.539301] SPR radius for FAST iterations: 25 (autodetect) [16:30:25 -163558.539301] Model parameter optimization (eps = 3.000000) [16:30:56 -163391.556082] FAST spr round 1 (radius: 25) [16:33:37 -150610.020659] FAST spr round 2 (radius: 25) [16:35:47 -149942.116189] FAST spr round 3 (radius: 25) [16:37:43 -149886.950743] FAST spr round 4 (radius: 25) [16:39:37 -149875.687434] FAST spr round 5 (radius: 25) [16:41:19 -149873.894363] FAST spr round 6 (radius: 25) [16:43:08 -149871.397981] FAST spr round 7 (radius: 25) [16:44:57 -149871.397651] Model parameter optimization (eps = 1.000000) [16:45:16 -149866.355902] SLOW spr round 1 (radius: 5) [16:47:21 -149818.638550] SLOW spr round 2 (radius: 5) [16:49:27 -149815.537288] SLOW spr round 3 (radius: 5) [16:51:28 -149815.535326] SLOW spr round 4 (radius: 10) [16:53:35 -149809.865314] SLOW spr round 5 (radius: 5) [16:56:10 -149806.086997] SLOW spr round 6 (radius: 5) [16:58:39 -149797.764002] SLOW spr round 7 (radius: 5) [17:00:58 -149794.416990] SLOW spr round 8 (radius: 5) [17:03:07 -149789.252163] SLOW spr round 9 (radius: 5) [17:05:14 -149786.916869] SLOW spr round 10 (radius: 5) [17:07:23 -149785.805762] SLOW spr round 11 (radius: 5) [17:09:31 -149785.293377] SLOW spr round 12 (radius: 5) [17:11:37 -149785.292858] SLOW spr round 13 (radius: 10) [17:13:43 -149784.271517] SLOW spr round 14 (radius: 5) [17:16:12 -149784.271083] SLOW spr round 15 (radius: 10) [17:18:32 -149784.271060] SLOW spr round 16 (radius: 15) [17:22:04 -149784.042522] SLOW spr round 17 (radius: 5) [17:24:52 -149783.993516] SLOW spr round 18 (radius: 10) [17:27:13 -149783.993012] SLOW spr round 19 (radius: 15) [17:30:21 -149783.992975] SLOW spr round 20 (radius: 20) [17:35:32 -149783.992964] SLOW spr round 21 (radius: 25) [17:42:24 -149783.992956] Model parameter optimization (eps = 0.100000) [17:42:36] ML tree search #14, logLikelihood: -149783.725171 [17:42:36 -453737.548687] Initial branch length optimization [17:42:39 -388996.869073] Model parameter optimization (eps = 10.000000) [17:43:28 -387152.034814] AUTODETECT spr round 1 (radius: 5) [17:45:32 -267257.694023] AUTODETECT spr round 2 (radius: 10) [17:47:51 -204204.464144] AUTODETECT spr round 3 (radius: 15) [17:50:39 -174040.175855] AUTODETECT spr round 4 (radius: 20) [17:53:45 -167065.574181] AUTODETECT spr round 5 (radius: 25) [17:57:33 -166348.399335] SPR radius for FAST iterations: 25 (autodetect) [17:57:33 -166348.399335] Model parameter optimization (eps = 3.000000) [17:58:04 -166256.499191] FAST spr round 1 (radius: 25) [18:00:59 -150465.592422] FAST spr round 2 (radius: 25) [18:03:23 -149916.450822] FAST spr round 3 (radius: 25) [18:05:20 -149880.411277] FAST spr round 4 (radius: 25) [18:07:06 -149855.811364] FAST spr round 5 (radius: 25) [18:08:45 -149855.810060] Model parameter optimization (eps = 1.000000) [18:09:08 -149842.296075] SLOW spr round 1 (radius: 5) [18:11:16 -149788.060199] SLOW spr round 2 (radius: 5) [18:13:20 -149786.674408] SLOW spr round 3 (radius: 5) [18:15:30 -149785.804185] SLOW spr round 4 (radius: 5) [18:17:34 -149785.802931] SLOW spr round 5 (radius: 10) [18:19:54 -149784.781369] SLOW spr round 6 (radius: 5) [18:22:28 -149784.781040] SLOW spr round 7 (radius: 10) [18:24:46 -149784.780884] SLOW spr round 8 (radius: 15) [18:28:00 -149784.780800] SLOW spr round 9 (radius: 20) [18:33:06 -149784.780750] SLOW spr round 10 (radius: 25) [18:39:32 -149784.780719] Model parameter optimization (eps = 0.100000) [18:39:47] ML tree search #15, logLikelihood: -149784.526319 [18:39:47 -453288.931727] Initial branch length optimization [18:39:49 -389960.635499] Model parameter optimization (eps = 10.000000) [18:40:29 -388114.404999] AUTODETECT spr round 1 (radius: 5) [18:42:28 -270111.778892] AUTODETECT spr round 2 (radius: 10) [18:44:47 -198984.395989] AUTODETECT spr round 3 (radius: 15) [18:47:12 -176439.019633] AUTODETECT spr round 4 (radius: 20) [18:50:00 -168399.196284] AUTODETECT spr round 5 (radius: 25) [18:53:26 -166907.783764] SPR radius for FAST iterations: 25 (autodetect) [18:53:26 -166907.783764] Model parameter optimization (eps = 3.000000) [18:53:48 -166782.802563] FAST spr round 1 (radius: 25) [18:56:29 -150585.166617] FAST spr round 2 (radius: 25) [18:58:43 -149958.458708] FAST spr round 3 (radius: 25) [19:00:49 -149846.599443] FAST spr round 4 (radius: 25) [19:02:39 -149843.027364] FAST spr round 5 (radius: 25) [19:04:18 -149843.025653] Model parameter optimization (eps = 1.000000) [19:04:42 -149833.115578] SLOW spr round 1 (radius: 5) [19:06:53 -149798.568497] SLOW spr round 2 (radius: 5) [19:09:09 -149791.904941] SLOW spr round 3 (radius: 5) [19:11:23 -149791.904130] SLOW spr round 4 (radius: 10) [19:13:31 -149785.495743] SLOW spr round 5 (radius: 5) [19:16:00 -149785.494679] SLOW spr round 6 (radius: 10) [19:18:20 -149785.277724] SLOW spr round 7 (radius: 5) [19:20:53 -149785.277518] SLOW spr round 8 (radius: 10) [19:23:22 -149785.277509] SLOW spr round 9 (radius: 15) [19:26:33 -149784.728346] SLOW spr round 10 (radius: 5) [19:29:05 -149784.728289] SLOW spr round 11 (radius: 10) [19:31:23 -149784.728287] SLOW spr round 12 (radius: 15) [19:34:26 -149784.728287] SLOW spr round 13 (radius: 20) [19:39:44 -149784.728286] SLOW spr round 14 (radius: 25) [19:46:36 -149784.728286] Model parameter optimization (eps = 0.100000) [19:46:45] ML tree search #16, logLikelihood: -149784.541287 [19:46:45 -453383.553300] Initial branch length optimization [19:46:49 -388466.824829] Model parameter optimization (eps = 10.000000) [19:47:26 -386639.470454] AUTODETECT spr round 1 (radius: 5) [19:49:32 -267731.267277] AUTODETECT spr round 2 (radius: 10) [19:51:49 -197796.100955] AUTODETECT spr round 3 (radius: 15) [19:54:04 -174698.355000] AUTODETECT spr round 4 (radius: 20) [19:56:46 -166325.243331] AUTODETECT spr round 5 (radius: 25) [20:00:23 -163893.052977] SPR radius for FAST iterations: 25 (autodetect) [20:00:23 -163893.052977] Model parameter optimization (eps = 3.000000) [20:00:52 -163763.935322] FAST spr round 1 (radius: 25) [20:03:40 -150431.528482] FAST spr round 2 (radius: 25) [20:05:44 -149877.843720] FAST spr round 3 (radius: 25) [20:07:35 -149844.456914] FAST spr round 4 (radius: 25) [20:09:17 -149839.171781] FAST spr round 5 (radius: 25) [20:10:57 -149839.158998] Model parameter optimization (eps = 1.000000) [20:11:15 -149831.783973] SLOW spr round 1 (radius: 5) [20:13:23 -149786.880224] SLOW spr round 2 (radius: 5) [20:15:30 -149782.635949] SLOW spr round 3 (radius: 5) [20:17:43 -149782.635765] SLOW spr round 4 (radius: 10) [20:19:56 -149780.643046] SLOW spr round 5 (radius: 5) [20:22:31 -149780.642853] SLOW spr round 6 (radius: 10) [20:24:59 -149780.642827] SLOW spr round 7 (radius: 15) [20:28:23 -149780.642815] SLOW spr round 8 (radius: 20) [20:33:20 -149780.642808] SLOW spr round 9 (radius: 25) [20:39:43 -149780.516132] SLOW spr round 10 (radius: 5) [20:42:38 -149780.516070] SLOW spr round 11 (radius: 10) [20:45:04 -149780.516068] SLOW spr round 12 (radius: 15) [20:48:11 -149780.516066] SLOW spr round 13 (radius: 20) [20:53:02 -149780.516065] SLOW spr round 14 (radius: 25) [20:59:40 -149780.516064] Model parameter optimization (eps = 0.100000) [20:59:48] ML tree search #17, logLikelihood: -149780.433867 [20:59:48 -449665.241583] Initial branch length optimization [20:59:51 -386301.748817] Model parameter optimization (eps = 10.000000) [21:00:28 -384495.462905] AUTODETECT spr round 1 (radius: 5) [21:02:25 -270742.610039] AUTODETECT spr round 2 (radius: 10) [21:04:49 -201778.281060] AUTODETECT spr round 3 (radius: 15) [21:07:11 -175466.234520] AUTODETECT spr round 4 (radius: 20) [21:10:23 -169041.099726] AUTODETECT spr round 5 (radius: 25) [21:13:51 -167750.611901] SPR radius for FAST iterations: 25 (autodetect) [21:13:51 -167750.611901] Model parameter optimization (eps = 3.000000) [21:14:13 -167644.158970] FAST spr round 1 (radius: 25) [21:17:07 -150471.878368] FAST spr round 2 (radius: 25) [21:19:24 -149930.543696] FAST spr round 3 (radius: 25) [21:21:21 -149874.713709] FAST spr round 4 (radius: 25) [21:23:07 -149871.699767] FAST spr round 5 (radius: 25) [21:24:45 -149871.688287] Model parameter optimization (eps = 1.000000) [21:25:10 -149854.066365] SLOW spr round 1 (radius: 5) [21:27:15 -149802.006814] SLOW spr round 2 (radius: 5) [21:29:20 -149790.498996] SLOW spr round 3 (radius: 5) [21:31:25 -149788.261372] SLOW spr round 4 (radius: 5) [21:33:25 -149788.260160] SLOW spr round 5 (radius: 10) [21:35:31 -149784.894576] SLOW spr round 6 (radius: 5) [21:38:04 -149784.894089] SLOW spr round 7 (radius: 10) [21:40:27 -149784.893801] SLOW spr round 8 (radius: 15) [21:43:37 -149784.430429] SLOW spr round 9 (radius: 5) [21:46:16 -149784.430318] SLOW spr round 10 (radius: 10) [21:48:43 -149784.430260] SLOW spr round 11 (radius: 15) [21:51:53 -149784.430222] SLOW spr round 12 (radius: 20) [21:56:55 -149784.430197] SLOW spr round 13 (radius: 25) [22:03:57 -149784.430180] Model parameter optimization (eps = 0.100000) [22:04:16] ML tree search #18, logLikelihood: -149782.907808 [22:04:16 -449614.641268] Initial branch length optimization [22:04:18 -386770.066904] Model parameter optimization (eps = 10.000000) [22:04:52 -384958.794638] AUTODETECT spr round 1 (radius: 5) [22:06:46 -265143.705950] AUTODETECT spr round 2 (radius: 10) [22:08:50 -195071.204353] AUTODETECT spr round 3 (radius: 15) [22:11:06 -172841.734672] AUTODETECT spr round 4 (radius: 20) [22:13:42 -169019.352673] AUTODETECT spr round 5 (radius: 25) [22:16:54 -168774.800090] SPR radius for FAST iterations: 25 (autodetect) [22:16:54 -168774.800090] Model parameter optimization (eps = 3.000000) [22:17:21 -168627.853507] FAST spr round 1 (radius: 25) [22:20:33 -150512.643027] FAST spr round 2 (radius: 25) [22:22:53 -149910.633900] FAST spr round 3 (radius: 25) [22:25:00 -149878.260382] FAST spr round 4 (radius: 25) [22:26:43 -149878.259699] Model parameter optimization (eps = 1.000000) [22:27:02 -149870.082994] SLOW spr round 1 (radius: 5) [22:29:13 -149817.487339] SLOW spr round 2 (radius: 5) [22:31:24 -149800.189166] SLOW spr round 3 (radius: 5) [22:33:26 -149800.186639] SLOW spr round 4 (radius: 10) [22:35:31 -149793.539319] SLOW spr round 5 (radius: 5) [22:38:02 -149788.141601] SLOW spr round 6 (radius: 5) [22:40:21 -149788.140973] SLOW spr round 7 (radius: 10) [22:42:31 -149788.140734] SLOW spr round 8 (radius: 15) [22:45:57 -149788.028728] SLOW spr round 9 (radius: 5) [22:48:30 -149786.406566] SLOW spr round 10 (radius: 5) [22:50:47 -149785.901721] SLOW spr round 11 (radius: 5) [22:52:56 -149785.901250] SLOW spr round 12 (radius: 10) [22:55:01 -149785.901225] SLOW spr round 13 (radius: 15) [22:58:32 -149785.901219] SLOW spr round 14 (radius: 20) [23:03:50 -149785.901216] SLOW spr round 15 (radius: 25) [23:10:31 -149785.901215] Model parameter optimization (eps = 0.100000) [23:10:43] ML tree search #19, logLikelihood: -149785.610714 [23:10:43 -454705.505322] Initial branch length optimization [23:10:46 -390475.455631] Model parameter optimization (eps = 10.000000) [23:11:28 -388542.888521] AUTODETECT spr round 1 (radius: 5) [23:13:24 -266441.706018] AUTODETECT spr round 2 (radius: 10) [23:15:29 -196556.740697] AUTODETECT spr round 3 (radius: 15) [23:17:46 -171716.380440] AUTODETECT spr round 4 (radius: 20) [23:20:40 -164846.310697] AUTODETECT spr round 5 (radius: 25) [23:24:07 -163477.731501] SPR radius for FAST iterations: 25 (autodetect) [23:24:07 -163477.731501] Model parameter optimization (eps = 3.000000) [23:24:39 -163365.007855] FAST spr round 1 (radius: 25) [23:27:14 -150644.165331] FAST spr round 2 (radius: 25) [23:29:20 -149897.024968] FAST spr round 3 (radius: 25) [23:31:13 -149850.502815] FAST spr round 4 (radius: 25) [23:32:54 -149843.836035] FAST spr round 5 (radius: 25) [23:34:32 -149842.203615] FAST spr round 6 (radius: 25) [23:36:10 -149842.203007] Model parameter optimization (eps = 1.000000) [23:36:26 -149832.875542] SLOW spr round 1 (radius: 5) [23:38:41 -149780.065695] SLOW spr round 2 (radius: 5) [23:41:00 -149777.042267] SLOW spr round 3 (radius: 5) [23:43:07 -149777.041471] SLOW spr round 4 (radius: 10) [23:45:25 -149775.821808] SLOW spr round 5 (radius: 5) [23:48:00 -149774.066514] SLOW spr round 6 (radius: 5) [23:50:13 -149774.065730] SLOW spr round 7 (radius: 10) [23:52:21 -149774.064934] SLOW spr round 8 (radius: 15) [23:55:41 -149774.064123] SLOW spr round 9 (radius: 20) [24:00:44 -149774.063389] SLOW spr round 10 (radius: 25) [24:07:40 -149774.063364] Model parameter optimization (eps = 0.100000) [24:07:53] ML tree search #20, logLikelihood: -149773.661245 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.344012,0.597923) (0.377392,0.800249) (0.217154,1.361854) (0.061442,3.199247) 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: -149756.776699 AIC score: 303019.553398 / AICc score: 6452543.553398 / BIC score: 310187.649064 Free parameters (model + branch lengths): 1753 WARNING: Number of free parameters (K=1753) is larger than alignment size (n=441). 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/Q2M3M2/3_mltree/Q2M3M2.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q2M3M2/3_mltree/Q2M3M2.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q2M3M2/3_mltree/Q2M3M2.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q2M3M2/3_mltree/Q2M3M2.raxml.log Analysis started: 04-Jul-2021 14:58:39 / finished: 05-Jul-2021 15:06:33 Elapsed time: 86873.790 seconds Consumed energy: 6742.976 Wh (= 34 km in an electric car, or 169 km with an e-scooter!)