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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 30-Jul-2021 10:16:24 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O14646/2_msa/O14646_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O14646/3_mltree/O14646 --seed 2 --threads 9 --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 (9 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O14646/2_msa/O14646_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1100 sites WARNING: Sequences tr_M3XXC0_M3XXC0_MUSPF_9669 and tr_G1M834_G1M834_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XXC0_M3XXC0_MUSPF_9669 and tr_A0A2U3ZLY1_A0A2U3ZLY1_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3XXC0_M3XXC0_MUSPF_9669 and tr_A0A2U3X8Q8_A0A2U3X8Q8_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3XXC0_M3XXC0_MUSPF_9669 and tr_A0A2Y9JRM9_A0A2Y9JRM9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3XXC0_M3XXC0_MUSPF_9669 and tr_A0A384CXB1_A0A384CXB1_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3Z1K2_M3Z1K2_MUSPF_9669 and tr_A0A2U3WHW2_A0A2U3WHW2_ODORO_9708 are exactly identical! WARNING: Sequences tr_J3K185_J3K185_COCIM_246410 and tr_A0A0J6YM07_A0A0J6YM07_COCIT_404692 are exactly identical! WARNING: Sequences tr_D8REK3_D8REK3_SELML_88036 and tr_D8RI44_D8RI44_SELML_88036 are exactly identical! WARNING: Sequences tr_A0A179UQN3_A0A179UQN3_BLAGS_559298 and tr_A0A179U2M9_A0A179U2M9_AJEDR_559297 are exactly identical! WARNING: Sequences tr_A0A2I3RQ86_A0A2I3RQ86_PANTR_9598 and sp_O14647_CHD2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3RQ86_A0A2I3RQ86_PANTR_9598 and tr_G7MW02_G7MW02_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3RQ86_A0A2I3RQ86_PANTR_9598 and tr_G7P9H9_G7P9H9_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2J8KJR8_A0A2J8KJR8_PANTR_9598 and sp_O14646_CHD1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8KJR8_A0A2J8KJR8_PANTR_9598 and tr_G7P802_G7P802_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2J8KJR8_A0A2J8KJR8_PANTR_9598 and tr_A0A096MMS1_A0A096MMS1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2J8KJR8_A0A2J8KJR8_PANTR_9598 and tr_A0A0D9RS42_A0A0D9RS42_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2J8KJR8_A0A2J8KJR8_PANTR_9598 and tr_A0A2K5LU02_A0A2K5LU02_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2J8KJR8_A0A2J8KJR8_PANTR_9598 and tr_A0A2K6EAC4_A0A2K6EAC4_MACNE_9545 are exactly identical! WARNING: Sequences tr_Q2U2M2_Q2U2M2_ASPOR_510516 and tr_A0A1S9DJ52_A0A1S9DJ52_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A0E0HLU3_A0A0E0HLU3_ORYNI_4536 and tr_A0A0D3GDJ7_A0A0D3GDJ7_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A2QQE1_A2QQE1_ASPNC_425011 and tr_G3YG83_G3YG83_ASPNA_380704 are exactly identical! WARNING: Sequences tr_G7XRH9_G7XRH9_ASPKW_1033177 and tr_A0A100IHW5_A0A100IHW5_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7XRH9_G7XRH9_ASPKW_1033177 and tr_A0A146FWZ6_A0A146FWZ6_9EURO_1069201 are exactly identical! WARNING: Sequences tr_F2SRN9_F2SRN9_TRIRC_559305 and tr_A0A178EYD5_A0A178EYD5_TRIRU_5551 are exactly identical! WARNING: Sequences tr_A0A0D2XCS6_A0A0D2XCS6_FUSO4_426428 and tr_X0D9H5_X0D9H5_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_A0A0D2XCS6_A0A0D2XCS6_FUSO4_426428 and tr_A0A2H3T4V5_A0A2H3T4V5_FUSOX_5507 are exactly identical! WARNING: Sequences tr_S0DZ71_S0DZ71_GIBF5_1279085 and tr_A0A365MQW4_A0A365MQW4_GIBIN_948311 are exactly identical! WARNING: Sequences tr_V2YXY8_V2YXY8_MONRO_1381753 and tr_A0A0W0FHB3_A0A0W0FHB3_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A094E702_A0A094E702_9PEZI_1420912 and tr_A0A2P2SXT7_A0A2P2SXT7_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0F8X7Y4_A0A0F8X7Y4_9EURO_308745 and tr_A0A2T5M1W6_A0A2T5M1W6_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A2I0MDG8_A0A2I0MDG8_COLLI_8932 and tr_A0A1V4JED6_A0A1V4JED6_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A117NP07_A0A117NP07_9EURO_48697 and tr_A0A1V6NET7_A0A1V6NET7_9EURO_60169 are exactly identical! WARNING: Sequences tr_I1RSI1_I1RSI1_GIBZE_229533 and tr_A0A2T4H1K1_A0A2T4H1K1_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A1R1XK28_A0A1R1XK28_9FUNG_133412 and tr_A0A1R1XYF0_A0A1R1XYF0_9FUNG_133412 are exactly identical! WARNING: Sequences tr_A0A2H3C893_A0A2H3C893_9AGAR_1076256 and tr_A0A284QM25_A0A284QM25_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2D0SQV4_A0A2D0SQV4_ICTPU_7998 and tr_A0A2D0SQV7_A0A2D0SQV7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4C6X5_A0A2U4C6X5_TURTR_9739 and tr_A0A2Y9Q649_A0A2Y9Q649_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4C6X5_A0A2U4C6X5_TURTR_9739 and tr_A0A2Y9TH35_A0A2Y9TH35_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3Y6D2_A0A2U3Y6D2_LEPWE_9713 and tr_A0A2Y9K0Q8_A0A2Y9K0Q8_ENHLU_391180 are exactly identical! WARNING: Duplicate sequences found: 39 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O14646/3_mltree/O14646.raxml.reduced.phy Alignment comprises 1 partitions and 1099 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 1100 / 1099 Gaps: 5.02 % Invariant sites: 2.64 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O14646/3_mltree/O14646.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 9 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 / 123 / 9840 [00:00:00] Data distribution: max. searches per worker: 20 Starting ML tree search with 20 distinct starting trees [00:00:00 -1772746.881879] Initial branch length optimization [00:00:12 -1501120.538870] Model parameter optimization (eps = 10.000000) [00:01:01 -1495404.383966] AUTODETECT spr round 1 (radius: 5) [00:03:40 -976863.181489] AUTODETECT spr round 2 (radius: 10) [00:06:39 -716928.998382] AUTODETECT spr round 3 (radius: 15) [00:09:38 -578940.537677] AUTODETECT spr round 4 (radius: 20) [00:13:14 -500960.487746] AUTODETECT spr round 5 (radius: 25) [00:17:10 -487900.145704] SPR radius for FAST iterations: 25 (autodetect) [00:17:10 -487900.145704] Model parameter optimization (eps = 3.000000) [00:17:29 -487875.768963] FAST spr round 1 (radius: 25) [00:20:25 -416995.175928] FAST spr round 2 (radius: 25) [00:22:42 -414025.642011] FAST spr round 3 (radius: 25) [00:24:47 -413883.567522] FAST spr round 4 (radius: 25) [00:26:38 -413874.204452] FAST spr round 5 (radius: 25) [00:28:27 -413874.204412] Model parameter optimization (eps = 1.000000) [00:28:40 -413870.144601] SLOW spr round 1 (radius: 5) [00:31:10 -413774.970264] SLOW spr round 2 (radius: 5) [00:33:34 -413767.910769] SLOW spr round 3 (radius: 5) [00:35:53 -413764.951270] SLOW spr round 4 (radius: 5) [00:38:09 -413764.951256] SLOW spr round 5 (radius: 10) [00:40:34 -413761.879179] SLOW spr round 6 (radius: 5) [00:43:26 -413759.406362] SLOW spr round 7 (radius: 5) [00:45:58 -413759.406220] SLOW spr round 8 (radius: 10) [00:48:25 -413759.406219] SLOW spr round 9 (radius: 15) [00:51:59 -413759.406219] SLOW spr round 10 (radius: 20) [00:56:55 -413759.406219] SLOW spr round 11 (radius: 25) [01:02:47 -413759.406219] Model parameter optimization (eps = 0.100000) [01:02:57] ML tree search #1, logLikelihood: -413759.157272 [01:02:57 -1761894.761570] Initial branch length optimization [01:03:04 -1494332.597606] Model parameter optimization (eps = 10.000000) [01:03:41 -1488736.057997] AUTODETECT spr round 1 (radius: 5) [01:06:24 -986115.534249] AUTODETECT spr round 2 (radius: 10) [01:09:35 -718068.068744] AUTODETECT spr round 3 (radius: 15) [01:12:28 -624829.296573] AUTODETECT spr round 4 (radius: 20) [01:16:01 -528952.625687] AUTODETECT spr round 5 (radius: 25) [01:19:16 -509431.675347] SPR radius for FAST iterations: 25 (autodetect) [01:19:16 -509431.675347] Model parameter optimization (eps = 3.000000) [01:19:32 -509427.822371] FAST spr round 1 (radius: 25) [01:22:18 -416984.229094] FAST spr round 2 (radius: 25) [01:24:30 -414049.281533] FAST spr round 3 (radius: 25) [01:26:34 -413891.026109] FAST spr round 4 (radius: 25) [01:28:28 -413858.170304] FAST spr round 5 (radius: 25) [01:30:17 -413858.169689] Model parameter optimization (eps = 1.000000) [01:30:31 -413853.109246] SLOW spr round 1 (radius: 5) [01:32:54 -413771.535205] SLOW spr round 2 (radius: 5) [01:35:15 -413770.779706] SLOW spr round 3 (radius: 5) [01:37:34 -413770.779658] SLOW spr round 4 (radius: 10) [01:39:59 -413767.506006] SLOW spr round 5 (radius: 5) [01:42:52 -413760.350125] SLOW spr round 6 (radius: 5) [01:45:25 -413760.349654] SLOW spr round 7 (radius: 10) [01:47:53 -413760.349644] SLOW spr round 8 (radius: 15) [01:51:29 -413760.349644] SLOW spr round 9 (radius: 20) [01:56:25 -413760.349644] SLOW spr round 10 (radius: 25) [02:02:20 -413760.349644] Model parameter optimization (eps = 0.100000) [02:02:31] ML tree search #2, logLikelihood: -413759.932941 [02:02:31 -1765849.518673] Initial branch length optimization [02:02:38 -1494010.513773] Model parameter optimization (eps = 10.000000) [02:03:35 -1488369.486851] AUTODETECT spr round 1 (radius: 5) [02:06:15 -979257.149825] AUTODETECT spr round 2 (radius: 10) [02:09:22 -730094.998805] AUTODETECT spr round 3 (radius: 15) [02:12:29 -645794.230583] AUTODETECT spr round 4 (radius: 20) [02:15:45 -547882.012631] AUTODETECT spr round 5 (radius: 25) [02:19:26 -524559.873702] SPR radius for FAST iterations: 25 (autodetect) [02:19:26 -524559.873702] Model parameter optimization (eps = 3.000000) [02:19:45 -524542.733209] FAST spr round 1 (radius: 25) [02:22:55 -425557.696312] FAST spr round 2 (radius: 25) [02:25:12 -414251.164155] FAST spr round 3 (radius: 25) [02:27:13 -413852.538846] FAST spr round 4 (radius: 25) [02:29:06 -413846.928426] FAST spr round 5 (radius: 25) [02:30:55 -413846.928375] Model parameter optimization (eps = 1.000000) [02:31:07 -413843.969563] SLOW spr round 1 (radius: 5) [02:33:30 -413762.191720] SLOW spr round 2 (radius: 5) [02:35:53 -413758.812838] SLOW spr round 3 (radius: 5) [02:38:11 -413758.812629] SLOW spr round 4 (radius: 10) [02:40:35 -413758.800293] SLOW spr round 5 (radius: 15) [02:44:15 -413758.800287] SLOW spr round 6 (radius: 20) [02:49:11 -413758.800287] SLOW spr round 7 (radius: 25) [02:55:08 -413758.800286] Model parameter optimization (eps = 0.100000) [02:55:19] ML tree search #3, logLikelihood: -413758.606709 [02:55:19 -1760257.187224] Initial branch length optimization [02:55:29 -1491259.220160] Model parameter optimization (eps = 10.000000) [02:56:38 -1485775.594070] AUTODETECT spr round 1 (radius: 5) [02:59:21 -977537.049260] AUTODETECT spr round 2 (radius: 10) [03:02:26 -726684.771635] AUTODETECT spr round 3 (radius: 15) [03:05:34 -599199.453170] AUTODETECT spr round 4 (radius: 20) [03:08:42 -534818.689328] AUTODETECT spr round 5 (radius: 25) [03:12:12 -510785.948270] SPR radius for FAST iterations: 25 (autodetect) [03:12:12 -510785.948270] Model parameter optimization (eps = 3.000000) [03:12:31 -510777.965923] FAST spr round 1 (radius: 25) [03:15:24 -416801.300482] FAST spr round 2 (radius: 25) [03:17:48 -414040.872589] FAST spr round 3 (radius: 25) [03:19:56 -413943.798860] FAST spr round 4 (radius: 25) [03:21:50 -413925.464058] FAST spr round 5 (radius: 25) [03:23:39 -413925.463854] Model parameter optimization (eps = 1.000000) [03:23:54 -413920.096680] SLOW spr round 1 (radius: 5) [03:26:27 -413789.066843] SLOW spr round 2 (radius: 5) [03:28:51 -413781.850512] SLOW spr round 3 (radius: 5) [03:31:09 -413781.849768] SLOW spr round 4 (radius: 10) [03:33:34 -413781.284916] SLOW spr round 5 (radius: 5) [03:36:26 -413781.284915] SLOW spr round 6 (radius: 10) [03:39:01 -413781.284915] SLOW spr round 7 (radius: 15) [03:42:32 -413781.284915] SLOW spr round 8 (radius: 20) [03:47:30 -413781.284915] SLOW spr round 9 (radius: 25) [03:53:27 -413781.284915] Model parameter optimization (eps = 0.100000) [03:53:38] ML tree search #4, logLikelihood: -413780.949170 [03:53:38 -1760665.301782] Initial branch length optimization [03:53:44 -1489436.262635] Model parameter optimization (eps = 10.000000) [03:54:18 -1483747.572093] AUTODETECT spr round 1 (radius: 5) [03:56:59 -992558.767591] AUTODETECT spr round 2 (radius: 10) [04:00:10 -730281.323987] AUTODETECT spr round 3 (radius: 15) [04:03:03 -606635.173548] AUTODETECT spr round 4 (radius: 20) [04:06:23 -560501.997524] AUTODETECT spr round 5 (radius: 25) [04:10:08 -531375.208741] SPR radius for FAST iterations: 25 (autodetect) [04:10:08 -531375.208741] Model parameter optimization (eps = 3.000000) [04:10:31 -531348.349187] FAST spr round 1 (radius: 25) [04:13:17 -422903.347423] FAST spr round 2 (radius: 25) [04:15:30 -414364.488626] FAST spr round 3 (radius: 25) [04:17:40 -413943.198171] FAST spr round 4 (radius: 25) [04:19:34 -413937.595805] FAST spr round 5 (radius: 25) [04:21:23 -413937.595767] Model parameter optimization (eps = 1.000000) [04:21:39 -413922.368899] SLOW spr round 1 (radius: 5) [04:24:05 -413814.651488] SLOW spr round 2 (radius: 5) [04:26:31 -413787.733063] SLOW spr round 3 (radius: 5) [04:28:55 -413771.409284] SLOW spr round 4 (radius: 5) [04:31:15 -413769.598817] SLOW spr round 5 (radius: 5) [04:33:32 -413769.598555] SLOW spr round 6 (radius: 10) [04:35:57 -413769.598549] SLOW spr round 7 (radius: 15) [04:39:36 -413769.598543] SLOW spr round 8 (radius: 20) [04:44:30 -413769.598542] SLOW spr round 9 (radius: 25) [04:50:26 -413769.598542] Model parameter optimization (eps = 0.100000) [04:50:39] ML tree search #5, logLikelihood: -413768.888590 [04:50:39 -1765847.803977] Initial branch length optimization [04:50:47 -1494514.412481] Model parameter optimization (eps = 10.000000) [04:51:24 -1488790.282132] AUTODETECT spr round 1 (radius: 5) [04:54:05 -974713.945164] AUTODETECT spr round 2 (radius: 10) [04:56:58 -719958.849287] AUTODETECT spr round 3 (radius: 15) [04:59:59 -587520.428882] AUTODETECT spr round 4 (radius: 20) [05:03:26 -535648.518657] AUTODETECT spr round 5 (radius: 25) [05:07:17 -501794.882934] SPR radius for FAST iterations: 25 (autodetect) [05:07:17 -501794.882934] Model parameter optimization (eps = 3.000000) [05:07:35 -501774.623241] FAST spr round 1 (radius: 25) [05:10:34 -419444.425135] FAST spr round 2 (radius: 25) [05:12:58 -414288.352656] FAST spr round 3 (radius: 25) [05:15:05 -413901.388173] FAST spr round 4 (radius: 25) [05:17:01 -413876.514471] FAST spr round 5 (radius: 25) [05:18:49 -413876.514407] Model parameter optimization (eps = 1.000000) [05:19:02 -413875.340653] SLOW spr round 1 (radius: 5) [05:21:33 -413796.936898] SLOW spr round 2 (radius: 5) [05:23:56 -413793.295162] SLOW spr round 3 (radius: 5) [05:26:14 -413793.295102] SLOW spr round 4 (radius: 10) [05:28:38 -413793.295102] SLOW spr round 5 (radius: 15) [05:32:19 -413793.110523] SLOW spr round 6 (radius: 5) [05:35:23 -413792.562633] SLOW spr round 7 (radius: 5) [05:38:04 -413791.203678] SLOW spr round 8 (radius: 5) [05:40:31 -413791.203677] SLOW spr round 9 (radius: 10) [05:42:57 -413791.203677] SLOW spr round 10 (radius: 15) [05:46:37 -413791.203677] SLOW spr round 11 (radius: 20) [05:51:34 -413791.203677] SLOW spr round 12 (radius: 25) [05:57:37 -413791.203677] Model parameter optimization (eps = 0.100000) [05:57:47] ML tree search #6, logLikelihood: -413791.040218 [05:57:47 -1763808.194042] Initial branch length optimization [05:57:58 -1497128.418719] Model parameter optimization (eps = 10.000000) [05:58:56 -1491355.755969] AUTODETECT spr round 1 (radius: 5) [06:01:38 -960947.221100] AUTODETECT spr round 2 (radius: 10) [06:04:37 -691436.665027] AUTODETECT spr round 3 (radius: 15) [06:07:35 -582118.920970] AUTODETECT spr round 4 (radius: 20) [06:11:05 -504183.016980] AUTODETECT spr round 5 (radius: 25) [06:14:58 -495089.515984] SPR radius for FAST iterations: 25 (autodetect) [06:14:58 -495089.515984] Model parameter optimization (eps = 3.000000) [06:15:15 -495072.783483] FAST spr round 1 (radius: 25) [06:18:11 -417575.697769] FAST spr round 2 (radius: 25) [06:20:32 -414154.693109] FAST spr round 3 (radius: 25) [06:22:37 -413916.571960] FAST spr round 4 (radius: 25) [06:24:36 -413886.741051] FAST spr round 5 (radius: 25) [06:26:25 -413879.595442] FAST spr round 6 (radius: 25) [06:28:07 -413879.595440] Model parameter optimization (eps = 1.000000) [06:28:20 -413877.283273] SLOW spr round 1 (radius: 5) [06:30:41 -413794.196466] SLOW spr round 2 (radius: 5) [06:33:01 -413779.528957] SLOW spr round 3 (radius: 5) [06:35:19 -413772.183645] SLOW spr round 4 (radius: 5) [06:37:32 -413772.183413] SLOW spr round 5 (radius: 10) [06:39:54 -413772.183409] SLOW spr round 6 (radius: 15) [06:43:28 -413772.183409] SLOW spr round 7 (radius: 20) [06:48:18 -413772.183409] SLOW spr round 8 (radius: 25) [06:54:11 -413772.183409] Model parameter optimization (eps = 0.100000) [06:54:20] ML tree search #7, logLikelihood: -413772.000182 [06:54:21 -1773091.731125] Initial branch length optimization [06:54:27 -1500595.756820] Model parameter optimization (eps = 10.000000) [06:55:05 -1494930.991693] AUTODETECT spr round 1 (radius: 5) [06:57:41 -979428.976483] AUTODETECT spr round 2 (radius: 10) [07:00:42 -680410.715065] AUTODETECT spr round 3 (radius: 15) [07:03:37 -549444.457777] AUTODETECT spr round 4 (radius: 20) [07:06:55 -495755.957930] AUTODETECT spr round 5 (radius: 25) [07:11:16 -489336.148406] SPR radius for FAST iterations: 25 (autodetect) [07:11:16 -489336.148406] Model parameter optimization (eps = 3.000000) [07:11:31 -489319.094296] FAST spr round 1 (radius: 25) [07:14:31 -416225.795241] FAST spr round 2 (radius: 25) [07:16:49 -414055.666146] FAST spr round 3 (radius: 25) [07:18:48 -413863.283446] FAST spr round 4 (radius: 25) [07:20:38 -413848.405585] FAST spr round 5 (radius: 25) [07:22:23 -413848.405496] Model parameter optimization (eps = 1.000000) [07:22:38 -413840.406355] SLOW spr round 1 (radius: 5) [07:25:00 -413766.668519] SLOW spr round 2 (radius: 5) [07:27:19 -413760.769294] SLOW spr round 3 (radius: 5) [07:29:35 -413760.768390] SLOW spr round 4 (radius: 10) [07:31:56 -413758.177735] SLOW spr round 5 (radius: 5) [07:34:43 -413758.176867] SLOW spr round 6 (radius: 10) [07:37:14 -413758.176866] SLOW spr round 7 (radius: 15) [07:40:40 -413758.176866] SLOW spr round 8 (radius: 20) [07:45:30 -413758.176866] SLOW spr round 9 (radius: 25) [07:51:17 -413758.176866] Model parameter optimization (eps = 0.100000) [07:51:24] ML tree search #8, logLikelihood: -413758.105308 [07:51:24 -1771141.724585] Initial branch length optimization [07:51:31 -1491508.659566] Model parameter optimization (eps = 10.000000) [07:52:12 -1485734.138470] AUTODETECT spr round 1 (radius: 5) [07:54:49 -996655.699037] AUTODETECT spr round 2 (radius: 10) [07:57:59 -722531.197014] AUTODETECT spr round 3 (radius: 15) [08:01:07 -573985.369081] AUTODETECT spr round 4 (radius: 20) [08:04:24 -508333.723841] AUTODETECT spr round 5 (radius: 25) [08:07:36 -492856.039512] SPR radius for FAST iterations: 25 (autodetect) [08:07:36 -492856.039512] Model parameter optimization (eps = 3.000000) [08:07:53 -492837.644467] FAST spr round 1 (radius: 25) [08:10:47 -418092.009407] FAST spr round 2 (radius: 25) [08:13:05 -414239.738183] FAST spr round 3 (radius: 25) [08:15:08 -413936.922258] FAST spr round 4 (radius: 25) [08:17:10 -413884.531760] FAST spr round 5 (radius: 25) [08:18:56 -413882.330984] FAST spr round 6 (radius: 25) [08:20:39 -413882.330959] Model parameter optimization (eps = 1.000000) [08:20:53 -413879.588890] SLOW spr round 1 (radius: 5) [08:23:27 -413772.882622] SLOW spr round 2 (radius: 5) [08:25:57 -413755.231860] SLOW spr round 3 (radius: 5) [08:28:12 -413752.575419] SLOW spr round 4 (radius: 5) [08:30:24 -413752.575364] SLOW spr round 5 (radius: 10) [08:32:44 -413752.575364] SLOW spr round 6 (radius: 15) [08:36:25 -413752.575364] SLOW spr round 7 (radius: 20) [08:41:16 -413752.575364] SLOW spr round 8 (radius: 25) [08:47:10 -413752.575364] Model parameter optimization (eps = 0.100000) [08:47:18] ML tree search #9, logLikelihood: -413752.398986 [08:47:18 -1774204.395680] Initial branch length optimization [08:47:26 -1496703.644558] Model parameter optimization (eps = 10.000000) [08:48:07 -1491075.406326] AUTODETECT spr round 1 (radius: 5) [08:50:46 -979715.342693] AUTODETECT spr round 2 (radius: 10) [08:53:38 -741513.223356] AUTODETECT spr round 3 (radius: 15) [08:56:41 -627591.088675] AUTODETECT spr round 4 (radius: 20) [08:59:47 -554072.248320] AUTODETECT spr round 5 (radius: 25) [09:03:07 -525523.464835] SPR radius for FAST iterations: 25 (autodetect) [09:03:07 -525523.464835] Model parameter optimization (eps = 3.000000) [09:03:26 -525490.613354] FAST spr round 1 (radius: 25) [09:06:31 -423519.491719] FAST spr round 2 (radius: 25) [09:08:51 -414928.269550] FAST spr round 3 (radius: 25) [09:10:48 -413947.153871] FAST spr round 4 (radius: 25) [09:12:41 -413908.562035] FAST spr round 5 (radius: 25) [09:14:28 -413900.722208] FAST spr round 6 (radius: 25) [09:16:12 -413896.286865] FAST spr round 7 (radius: 25) [09:17:55 -413896.286818] Model parameter optimization (eps = 1.000000) [09:18:07 -413894.763463] SLOW spr round 1 (radius: 5) [09:20:30 -413777.101686] SLOW spr round 2 (radius: 5) [09:22:48 -413766.858511] SLOW spr round 3 (radius: 5) [09:25:02 -413766.530991] SLOW spr round 4 (radius: 5) [09:27:15 -413766.530991] SLOW spr round 5 (radius: 10) [09:29:40 -413766.530991] SLOW spr round 6 (radius: 15) [09:33:14 -413766.530991] SLOW spr round 7 (radius: 20) [09:37:59 -413766.530991] SLOW spr round 8 (radius: 25) [09:43:44 -413766.530991] Model parameter optimization (eps = 0.100000) [09:43:53] ML tree search #10, logLikelihood: -413766.343793 [09:43:53 -1765355.684580] Initial branch length optimization [09:43:59 -1503978.395348] Model parameter optimization (eps = 10.000000) [09:44:36 -1498123.964270] AUTODETECT spr round 1 (radius: 5) [09:47:13 -968320.714110] AUTODETECT spr round 2 (radius: 10) [09:50:14 -676202.130502] AUTODETECT spr round 3 (radius: 15) [09:52:54 -558966.751243] AUTODETECT spr round 4 (radius: 20) [09:56:13 -516736.172391] AUTODETECT spr round 5 (radius: 25) [09:59:49 -496893.505948] SPR radius for FAST iterations: 25 (autodetect) [09:59:49 -496893.505948] Model parameter optimization (eps = 3.000000) [10:00:11 -496818.258208] FAST spr round 1 (radius: 25) [10:02:56 -418900.513991] FAST spr round 2 (radius: 25) [10:05:12 -414218.958807] FAST spr round 3 (radius: 25) [10:07:14 -413886.021561] FAST spr round 4 (radius: 25) [10:09:05 -413865.203730] FAST spr round 5 (radius: 25) [10:10:49 -413862.271117] FAST spr round 6 (radius: 25) [10:12:32 -413862.271109] Model parameter optimization (eps = 1.000000) [10:12:44 -413857.681129] SLOW spr round 1 (radius: 5) [10:15:06 -413772.302935] SLOW spr round 2 (radius: 5) [10:17:24 -413766.562054] SLOW spr round 3 (radius: 5) [10:19:38 -413765.278535] SLOW spr round 4 (radius: 5) [10:21:50 -413765.278472] SLOW spr round 5 (radius: 10) [10:24:10 -413765.278471] SLOW spr round 6 (radius: 15) [10:27:43 -413765.278471] SLOW spr round 7 (radius: 20) [10:32:25 -413765.278471] SLOW spr round 8 (radius: 25) [10:38:01 -413765.278471] Model parameter optimization (eps = 0.100000) [10:38:11] ML tree search #11, logLikelihood: -413765.140586 [10:38:11 -1766158.772513] Initial branch length optimization [10:38:22 -1495976.485721] Model parameter optimization (eps = 10.000000) [10:38:59 -1490438.715170] AUTODETECT spr round 1 (radius: 5) [10:41:35 -978087.677574] AUTODETECT spr round 2 (radius: 10) [10:44:35 -734060.650925] AUTODETECT spr round 3 (radius: 15) [10:47:47 -612239.014404] AUTODETECT spr round 4 (radius: 20) [10:51:07 -552236.720340] AUTODETECT spr round 5 (radius: 25) [10:54:33 -515504.242662] SPR radius for FAST iterations: 25 (autodetect) [10:54:33 -515504.242662] Model parameter optimization (eps = 3.000000) [10:54:50 -515496.632550] FAST spr round 1 (radius: 25) [10:57:45 -418370.502562] FAST spr round 2 (radius: 25) [11:00:01 -414182.363320] FAST spr round 3 (radius: 25) [11:02:07 -413921.223474] FAST spr round 4 (radius: 25) [11:03:59 -413881.527621] FAST spr round 5 (radius: 25) [11:05:45 -413865.804590] FAST spr round 6 (radius: 25) [11:07:29 -413865.804221] Model parameter optimization (eps = 1.000000) [11:07:43 -413861.413021] SLOW spr round 1 (radius: 5) [11:10:07 -413773.432611] SLOW spr round 2 (radius: 5) [11:12:24 -413758.296558] SLOW spr round 3 (radius: 5) [11:14:38 -413758.296438] SLOW spr round 4 (radius: 10) [11:16:59 -413756.406039] SLOW spr round 5 (radius: 5) [11:19:46 -413756.405295] SLOW spr round 6 (radius: 10) [11:22:16 -413756.405295] SLOW spr round 7 (radius: 15) [11:25:45 -413756.405295] SLOW spr round 8 (radius: 20) [11:30:41 -413756.405295] SLOW spr round 9 (radius: 25) [11:36:40 -413756.405295] Model parameter optimization (eps = 0.100000) [11:36:47] ML tree search #12, logLikelihood: -413756.334582 [11:36:47 -1768269.024597] Initial branch length optimization [11:36:56 -1501542.312491] Model parameter optimization (eps = 10.000000) [11:37:34 -1495821.896792] AUTODETECT spr round 1 (radius: 5) [11:40:12 -975875.332744] AUTODETECT spr round 2 (radius: 10) [11:43:12 -724209.952149] AUTODETECT spr round 3 (radius: 15) [11:46:06 -586666.541789] AUTODETECT spr round 4 (radius: 20) [11:49:19 -516971.765114] AUTODETECT spr round 5 (radius: 25) [11:53:05 -500426.597145] SPR radius for FAST iterations: 25 (autodetect) [11:53:05 -500426.597145] Model parameter optimization (eps = 3.000000) [11:53:15 -500420.212283] FAST spr round 1 (radius: 25) [11:55:59 -416191.893000] FAST spr round 2 (radius: 25) [11:58:07 -414007.658750] FAST spr round 3 (radius: 25) [12:00:05 -413940.800988] FAST spr round 4 (radius: 25) [12:01:56 -413913.809853] FAST spr round 5 (radius: 25) [12:03:40 -413911.699472] FAST spr round 6 (radius: 25) [12:05:23 -413911.699436] Model parameter optimization (eps = 1.000000) [12:05:35 -413905.383442] SLOW spr round 1 (radius: 5) [12:07:52 -413792.292377] SLOW spr round 2 (radius: 5) [12:10:09 -413773.821520] SLOW spr round 3 (radius: 5) [12:12:26 -413773.294793] SLOW spr round 4 (radius: 5) [12:14:39 -413773.294782] SLOW spr round 5 (radius: 10) [12:16:59 -413771.749317] SLOW spr round 6 (radius: 5) [12:19:52 -413764.716049] SLOW spr round 7 (radius: 5) [12:22:21 -413764.713453] SLOW spr round 8 (radius: 10) [12:24:44 -413764.713451] SLOW spr round 9 (radius: 15) [12:28:17 -413764.713451] SLOW spr round 10 (radius: 20) [12:33:10 -413764.713451] SLOW spr round 11 (radius: 25) [12:38:57 -413764.713451] Model parameter optimization (eps = 0.100000) [12:39:09] ML tree search #13, logLikelihood: -413764.027294 [12:39:10 -1773449.469555] Initial branch length optimization [12:39:17 -1490191.778561] Model parameter optimization (eps = 10.000000) [12:39:52 -1484728.965802] AUTODETECT spr round 1 (radius: 5) [12:42:31 -963858.304926] AUTODETECT spr round 2 (radius: 10) [12:45:35 -712761.286981] AUTODETECT spr round 3 (radius: 15) [12:48:32 -614600.671698] AUTODETECT spr round 4 (radius: 20) [12:52:06 -534198.705055] AUTODETECT spr round 5 (radius: 25) [12:55:43 -503151.272782] SPR radius for FAST iterations: 25 (autodetect) [12:55:43 -503151.272782] Model parameter optimization (eps = 3.000000) [12:56:02 -503139.344571] FAST spr round 1 (radius: 25) [12:58:54 -418416.173617] FAST spr round 2 (radius: 25) [13:01:13 -414260.078890] FAST spr round 3 (radius: 25) [13:03:17 -413914.285059] FAST spr round 4 (radius: 25) [13:05:09 -413879.742239] FAST spr round 5 (radius: 25) [13:06:55 -413879.742230] Model parameter optimization (eps = 1.000000) [13:07:11 -413876.349149] SLOW spr round 1 (radius: 5) [13:09:36 -413783.281088] SLOW spr round 2 (radius: 5) [13:11:58 -413765.229882] SLOW spr round 3 (radius: 5) [13:14:13 -413765.229777] SLOW spr round 4 (radius: 10) [13:16:35 -413759.593947] SLOW spr round 5 (radius: 5) [13:19:24 -413754.906468] SLOW spr round 6 (radius: 5) [13:21:54 -413754.697532] SLOW spr round 7 (radius: 5) [13:24:14 -413754.024453] SLOW spr round 8 (radius: 5) [13:26:29 -413754.023626] SLOW spr round 9 (radius: 10) [13:28:53 -413754.023626] SLOW spr round 10 (radius: 15) [13:32:28 -413754.023626] SLOW spr round 11 (radius: 20) [13:37:16 -413754.023626] SLOW spr round 12 (radius: 25) [13:43:02 -413754.023626] Model parameter optimization (eps = 0.100000) [13:43:13] ML tree search #14, logLikelihood: -413753.487565 [13:43:13 -1771800.529680] Initial branch length optimization [13:43:22 -1494190.745065] Model parameter optimization (eps = 10.000000) [13:44:26 -1488534.440795] AUTODETECT spr round 1 (radius: 5) [13:47:03 -979003.345348] AUTODETECT spr round 2 (radius: 10) [13:49:56 -709090.970308] AUTODETECT spr round 3 (radius: 15) [13:52:58 -547402.399404] AUTODETECT spr round 4 (radius: 20) [13:56:09 -506147.277268] AUTODETECT spr round 5 (radius: 25) [13:59:40 -497395.372951] SPR radius for FAST iterations: 25 (autodetect) [13:59:40 -497395.372951] Model parameter optimization (eps = 3.000000) [14:00:00 -497378.464239] FAST spr round 1 (radius: 25) [14:02:50 -416789.915925] FAST spr round 2 (radius: 25) [14:05:05 -414074.402030] FAST spr round 3 (radius: 25) [14:07:10 -413899.619800] FAST spr round 4 (radius: 25) [14:08:59 -413883.088912] FAST spr round 5 (radius: 25) [14:10:43 -413883.088838] Model parameter optimization (eps = 1.000000) [14:10:54 -413880.947289] SLOW spr round 1 (radius: 5) [14:13:24 -413770.763587] SLOW spr round 2 (radius: 5) [14:15:43 -413752.564006] SLOW spr round 3 (radius: 5) [14:17:58 -413748.917462] SLOW spr round 4 (radius: 5) [14:20:12 -413748.917097] SLOW spr round 5 (radius: 10) [14:22:32 -413748.917091] SLOW spr round 6 (radius: 15) [14:26:08 -413748.917090] SLOW spr round 7 (radius: 20) [14:31:01 -413748.917090] SLOW spr round 8 (radius: 25) [14:36:54 -413748.917090] Model parameter optimization (eps = 0.100000) [14:37:04] ML tree search #15, logLikelihood: -413748.705904 [14:37:04 -1753248.921077] Initial branch length optimization [14:37:14 -1485472.630178] Model parameter optimization (eps = 10.000000) [14:38:03 -1479827.239464] AUTODETECT spr round 1 (radius: 5) [14:40:41 -994976.283035] AUTODETECT spr round 2 (radius: 10) [14:43:50 -739786.295737] AUTODETECT spr round 3 (radius: 15) [14:46:56 -563899.385683] AUTODETECT spr round 4 (radius: 20) [14:50:03 -498387.353306] AUTODETECT spr round 5 (radius: 25) [14:53:54 -492467.405368] SPR radius for FAST iterations: 25 (autodetect) [14:53:54 -492467.405368] Model parameter optimization (eps = 3.000000) [14:54:02 -492463.699621] FAST spr round 1 (radius: 25) [14:56:57 -416255.516807] FAST spr round 2 (radius: 25) [14:59:16 -414190.383335] FAST spr round 3 (radius: 25) [15:01:19 -413970.815789] FAST spr round 4 (radius: 25) [15:03:11 -413908.898375] FAST spr round 5 (radius: 25) [15:04:57 -413896.266440] FAST spr round 6 (radius: 25) [15:06:40 -413896.266421] Model parameter optimization (eps = 1.000000) [15:06:56 -413884.046021] SLOW spr round 1 (radius: 5) [15:09:21 -413775.407629] SLOW spr round 2 (radius: 5) [15:11:40 -413771.150661] SLOW spr round 3 (radius: 5) [15:13:54 -413771.149828] SLOW spr round 4 (radius: 10) [15:16:15 -413771.149827] SLOW spr round 5 (radius: 15) [15:19:51 -413771.149827] SLOW spr round 6 (radius: 20) [15:24:43 -413771.149827] SLOW spr round 7 (radius: 25) [15:30:38 -413771.149827] Model parameter optimization (eps = 0.100000) [15:30:46] ML tree search #16, logLikelihood: -413770.999337 [15:30:46 -1773417.507957] Initial branch length optimization [15:30:52 -1502241.760894] Model parameter optimization (eps = 10.000000) [15:31:27 -1496429.760261] AUTODETECT spr round 1 (radius: 5) [15:34:05 -987344.520246] AUTODETECT spr round 2 (radius: 10) [15:37:02 -700279.740327] AUTODETECT spr round 3 (radius: 15) [15:39:46 -597945.780754] AUTODETECT spr round 4 (radius: 20) [15:43:02 -528393.495183] AUTODETECT spr round 5 (radius: 25) [15:46:41 -503327.865626] SPR radius for FAST iterations: 25 (autodetect) [15:46:41 -503327.865626] Model parameter optimization (eps = 3.000000) [15:46:59 -503318.768232] FAST spr round 1 (radius: 25) [15:49:52 -417015.536167] FAST spr round 2 (radius: 25) [15:52:09 -414090.084895] FAST spr round 3 (radius: 25) [15:54:12 -413884.063771] FAST spr round 4 (radius: 25) [15:56:01 -413875.167268] FAST spr round 5 (radius: 25) [15:57:46 -413875.167266] Model parameter optimization (eps = 1.000000) [15:57:58 -413872.815453] SLOW spr round 1 (radius: 5) [16:00:17 -413774.392921] SLOW spr round 2 (radius: 5) [16:02:36 -413762.056303] SLOW spr round 3 (radius: 5) [16:04:51 -413761.728536] SLOW spr round 4 (radius: 5) [16:07:05 -413761.727823] SLOW spr round 5 (radius: 10) [16:09:26 -413759.311748] SLOW spr round 6 (radius: 5) [16:12:13 -413759.311717] SLOW spr round 7 (radius: 10) [16:14:43 -413759.311717] SLOW spr round 8 (radius: 15) [16:18:09 -413759.311717] SLOW spr round 9 (radius: 20) [16:22:58 -413759.311711] SLOW spr round 10 (radius: 25) [16:28:40 -413759.311711] Model parameter optimization (eps = 0.100000) [16:28:49] ML tree search #17, logLikelihood: -413759.025016 [16:28:49 -1774325.658379] Initial branch length optimization [16:28:58 -1503118.164099] Model parameter optimization (eps = 10.000000) [16:29:47 -1497400.848528] AUTODETECT spr round 1 (radius: 5) [16:32:24 -994536.560468] AUTODETECT spr round 2 (radius: 10) [16:35:32 -699247.747877] AUTODETECT spr round 3 (radius: 15) [16:38:27 -598494.356119] AUTODETECT spr round 4 (radius: 20) [16:41:35 -526482.003766] AUTODETECT spr round 5 (radius: 25) [16:45:03 -512405.238162] SPR radius for FAST iterations: 25 (autodetect) [16:45:03 -512405.238162] Model parameter optimization (eps = 3.000000) [16:45:20 -512389.335699] FAST spr round 1 (radius: 25) [16:48:10 -417571.952338] FAST spr round 2 (radius: 25) [16:50:28 -414092.595595] FAST spr round 3 (radius: 25) [16:52:35 -413960.477663] FAST spr round 4 (radius: 25) [16:54:32 -413916.239803] FAST spr round 5 (radius: 25) [16:56:19 -413914.406619] FAST spr round 6 (radius: 25) [16:58:03 -413914.406573] Model parameter optimization (eps = 1.000000) [16:58:18 -413903.844603] SLOW spr round 1 (radius: 5) [17:00:45 -413793.907108] SLOW spr round 2 (radius: 5) [17:03:07 -413778.009191] SLOW spr round 3 (radius: 5) [17:05:24 -413773.748888] SLOW spr round 4 (radius: 5) [17:07:38 -413772.577505] SLOW spr round 5 (radius: 5) [17:09:53 -413772.576859] SLOW spr round 6 (radius: 10) [17:12:13 -413772.018840] SLOW spr round 7 (radius: 5) [17:15:02 -413772.018840] SLOW spr round 8 (radius: 10) [17:17:32 -413772.018840] SLOW spr round 9 (radius: 15) [17:21:01 -413772.018833] SLOW spr round 10 (radius: 20) [17:25:52 -413772.018833] SLOW spr round 11 (radius: 25) [17:31:39 -413772.018833] Model parameter optimization (eps = 0.100000) [17:31:51] ML tree search #18, logLikelihood: -413771.830071 [17:31:51 -1776164.783206] Initial branch length optimization [17:31:59 -1498329.245553] Model parameter optimization (eps = 10.000000) [17:32:40 -1492645.559556] AUTODETECT spr round 1 (radius: 5) [17:35:19 -1003135.416475] AUTODETECT spr round 2 (radius: 10) [17:38:29 -735483.850393] AUTODETECT spr round 3 (radius: 15) [17:41:29 -617645.176827] AUTODETECT spr round 4 (radius: 20) [17:44:44 -553365.608372] AUTODETECT spr round 5 (radius: 25) [17:48:08 -521558.786245] SPR radius for FAST iterations: 25 (autodetect) [17:48:08 -521558.786245] Model parameter optimization (eps = 3.000000) [17:48:27 -521542.064744] FAST spr round 1 (radius: 25) [17:51:27 -417974.337115] FAST spr round 2 (radius: 25) [17:53:51 -414162.656747] FAST spr round 3 (radius: 25) [17:55:56 -413910.759770] FAST spr round 4 (radius: 25) [17:57:46 -413896.746455] FAST spr round 5 (radius: 25) [17:59:32 -413893.817144] FAST spr round 6 (radius: 25) [18:01:16 -413889.869078] FAST spr round 7 (radius: 25) [18:02:59 -413889.869078] Model parameter optimization (eps = 1.000000) [18:03:13 -413888.086002] SLOW spr round 1 (radius: 5) [18:05:35 -413783.376836] SLOW spr round 2 (radius: 5) [18:07:57 -413770.025482] SLOW spr round 3 (radius: 5) [18:10:10 -413770.025451] SLOW spr round 4 (radius: 10) [18:12:30 -413769.697136] SLOW spr round 5 (radius: 5) [18:15:17 -413769.697130] SLOW spr round 6 (radius: 10) [18:17:47 -413769.697130] SLOW spr round 7 (radius: 15) [18:21:16 -413769.697130] SLOW spr round 8 (radius: 20) [18:26:09 -413769.697130] SLOW spr round 9 (radius: 25) [18:31:57 -413769.697130] Model parameter optimization (eps = 0.100000) [18:32:08] ML tree search #19, logLikelihood: -413768.863576 [18:32:08 -1773089.251248] Initial branch length optimization [18:32:18 -1500186.035985] Model parameter optimization (eps = 10.000000) [18:33:11 -1494715.271251] AUTODETECT spr round 1 (radius: 5) [18:35:44 -976755.429441] AUTODETECT spr round 2 (radius: 10) [18:38:36 -702621.042747] AUTODETECT spr round 3 (radius: 15) [18:41:28 -583495.575594] AUTODETECT spr round 4 (radius: 20) [18:44:32 -539884.133704] AUTODETECT spr round 5 (radius: 25) [18:48:06 -512770.458265] SPR radius for FAST iterations: 25 (autodetect) [18:48:06 -512770.458265] Model parameter optimization (eps = 3.000000) [18:48:22 -512758.051756] FAST spr round 1 (radius: 25) [18:51:16 -420512.748589] FAST spr round 2 (radius: 25) [18:53:34 -414327.829031] FAST spr round 3 (radius: 25) [18:55:33 -413889.462072] FAST spr round 4 (radius: 25) [18:57:21 -413884.212099] FAST spr round 5 (radius: 25) [18:59:06 -413884.212060] Model parameter optimization (eps = 1.000000) [18:59:17 -413882.371743] SLOW spr round 1 (radius: 5) [19:01:41 -413782.553325] SLOW spr round 2 (radius: 5) [19:03:59 -413770.301433] SLOW spr round 3 (radius: 5) [19:06:13 -413770.301338] SLOW spr round 4 (radius: 10) [19:08:32 -413770.288985] SLOW spr round 5 (radius: 15) [19:12:04 -413770.288979] SLOW spr round 6 (radius: 20) [19:16:50 -413770.288979] SLOW spr round 7 (radius: 25) [19:22:34 -413770.288979] Model parameter optimization (eps = 0.100000) [19:22:43] ML tree search #20, logLikelihood: -413770.171113 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.221302,0.223887) (0.226541,0.353819) (0.276095,0.999502) (0.276062,2.152928) 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: -413748.705904 AIC score: 831507.411808 / AICc score: 8875567.411808 / BIC score: 841538.558053 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=1100). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O14646/3_mltree/O14646.raxml.bestTree All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O14646/3_mltree/O14646.raxml.mlTrees Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O14646/3_mltree/O14646.raxml.bestModel Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O14646/3_mltree/O14646.raxml.log Analysis started: 30-Jul-2021 10:16:24 / finished: 31-Jul-2021 05:39:07 Elapsed time: 69763.454 seconds