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 13-Jul-2021 16:15:04 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q02297/2_msa/Q02297_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q02297/3_mltree/Q02297 --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: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q02297/2_msa/Q02297_trimmed_msa.fasta [00:00:00] Loaded alignment with 361 taxa and 879 sites WARNING: Sequences tr_F1NUK2_F1NUK2_CHICK_9031 and tr_G1MRS6_G1MRS6_MELGA_9103 are exactly identical! WARNING: Sequences tr_A0A2I2Z3C8_A0A2I2Z3C8_GORGO_9595 and tr_A0A2I3TS79_A0A2I3TS79_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SF73_G3SF73_GORGO_9595 and sp_Q5IS61_OPCM_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SF73_G3SF73_GORGO_9595 and sp_Q14982_OPCM_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F6T2Z6_F6T2Z6_MACMU_9544 and tr_A0A2I3LQL2_A0A2I3LQL2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6T2Z6_F6T2Z6_MACMU_9544 and tr_A0A2K5P2E7_A0A2K5P2E7_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6WLQ2_F6WLQ2_MACMU_9544 and tr_G7PPV6_G7PPV6_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6WLQ2_F6WLQ2_MACMU_9544 and tr_A0A2I3ME37_A0A2I3ME37_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6WLQ2_F6WLQ2_MACMU_9544 and tr_A0A2K5P1C9_A0A2K5P1C9_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6WLQ2_F6WLQ2_MACMU_9544 and tr_A0A2K6ANU4_A0A2K6ANU4_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HH69_F7HH69_MACMU_9544 and tr_A0A2I3M4S1_A0A2I3M4S1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HH69_F7HH69_MACMU_9544 and tr_A0A2K5MWM6_A0A2K5MWM6_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HH69_F7HH69_MACMU_9544 and tr_A0A2K5YYQ3_A0A2K5YYQ3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A091JEX3_A0A091JEX3_EGRGA_188379 and tr_A0A087R5W4_A0A087R5W4_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JEX3_A0A091JEX3_EGRGA_188379 and tr_A0A0A0AXT3_A0A0A0AXT3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A226NE45_A0A226NE45_CALSU_9009 and tr_A0A226PME5_A0A226PME5_COLVI_9014 are exactly identical! WARNING: Duplicate sequences found: 16 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/Q02297/3_mltree/Q02297.raxml.reduced.phy Alignment comprises 1 partitions and 879 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 879 / 879 Gaps: 45.16 % Invariant sites: 0.11 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q02297/3_mltree/Q02297.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 361 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 98 / 7840 [00:00:00] Data distribution: max. searches per worker: 20 Starting ML tree search with 20 distinct starting trees [00:00:00 -323205.236807] Initial branch length optimization [00:00:02 -266047.717746] Model parameter optimization (eps = 10.000000) [00:00:34 -264453.465520] AUTODETECT spr round 1 (radius: 5) [00:01:08 -153178.065463] AUTODETECT spr round 2 (radius: 10) [00:01:52 -104031.967101] AUTODETECT spr round 3 (radius: 15) [00:02:49 -87599.989321] AUTODETECT spr round 4 (radius: 20) [00:03:58 -85610.191687] AUTODETECT spr round 5 (radius: 25) [00:05:11 -85550.301112] SPR radius for FAST iterations: 25 (autodetect) [00:05:11 -85550.301112] Model parameter optimization (eps = 3.000000) [00:05:31 -85107.419006] FAST spr round 1 (radius: 25) [00:06:14 -78824.993378] FAST spr round 2 (radius: 25) [00:06:53 -78470.131713] FAST spr round 3 (radius: 25) [00:07:26 -78455.820228] FAST spr round 4 (radius: 25) [00:07:55 -78441.954746] FAST spr round 5 (radius: 25) [00:08:23 -78433.353616] FAST spr round 6 (radius: 25) [00:08:51 -78433.134177] FAST spr round 7 (radius: 25) [00:09:19 -78433.134141] Model parameter optimization (eps = 1.000000) [00:09:28 -78430.503590] SLOW spr round 1 (radius: 5) [00:10:16 -78422.473203] SLOW spr round 2 (radius: 5) [00:11:00 -78422.472630] SLOW spr round 3 (radius: 10) [00:11:47 -78421.821847] SLOW spr round 4 (radius: 5) [00:12:51 -78421.821775] SLOW spr round 5 (radius: 10) [00:13:47 -78421.821736] SLOW spr round 6 (radius: 15) [00:15:19 -78419.276835] SLOW spr round 7 (radius: 5) [00:16:33 -78413.799539] SLOW spr round 8 (radius: 5) [00:17:30 -78413.423917] SLOW spr round 9 (radius: 5) [00:18:19 -78413.423588] SLOW spr round 10 (radius: 10) [00:19:07 -78413.423477] SLOW spr round 11 (radius: 15) [00:20:40 -78413.291091] SLOW spr round 12 (radius: 5) [00:21:42 -78413.261637] SLOW spr round 13 (radius: 10) [00:22:43 -78413.261513] SLOW spr round 14 (radius: 15) [00:24:11 -78413.261479] SLOW spr round 15 (radius: 20) [00:26:14 -78413.261445] SLOW spr round 16 (radius: 25) [00:28:31 -78379.989954] SLOW spr round 17 (radius: 5) [00:29:42 -78379.085141] SLOW spr round 18 (radius: 5) [00:30:17 -78379.085103] SLOW spr round 19 (radius: 10) [00:31:02 -78379.085071] SLOW spr round 20 (radius: 15) [00:32:33 -78379.085039] SLOW spr round 21 (radius: 20) [00:34:36 -78379.085008] SLOW spr round 22 (radius: 25) [00:36:52 -78379.084976] Model parameter optimization (eps = 0.100000) [00:36:57] ML tree search #1, logLikelihood: -78379.025099 [00:36:57 -326295.512667] Initial branch length optimization [00:36:59 -268702.271186] Model parameter optimization (eps = 10.000000) [00:37:35 -266875.262386] AUTODETECT spr round 1 (radius: 5) [00:38:09 -148386.780164] AUTODETECT spr round 2 (radius: 10) [00:38:51 -106947.664081] AUTODETECT spr round 3 (radius: 15) [00:39:41 -90174.223707] AUTODETECT spr round 4 (radius: 20) [00:40:35 -87747.362127] AUTODETECT spr round 5 (radius: 25) [00:41:41 -87346.610889] SPR radius for FAST iterations: 25 (autodetect) [00:41:41 -87346.610889] Model parameter optimization (eps = 3.000000) [00:42:03 -86950.133450] FAST spr round 1 (radius: 25) [00:42:54 -78929.510870] FAST spr round 2 (radius: 25) [00:43:36 -78569.497787] FAST spr round 3 (radius: 25) [00:44:13 -78531.108359] FAST spr round 4 (radius: 25) [00:44:45 -78524.620306] FAST spr round 5 (radius: 25) [00:45:13 -78524.618583] Model parameter optimization (eps = 1.000000) [00:45:21 -78522.712952] SLOW spr round 1 (radius: 5) [00:46:10 -78510.693991] SLOW spr round 2 (radius: 5) [00:46:55 -78510.682567] SLOW spr round 3 (radius: 10) [00:47:43 -78510.682163] SLOW spr round 4 (radius: 15) [00:49:03 -78510.681811] SLOW spr round 5 (radius: 20) [00:50:39 -78477.524162] SLOW spr round 6 (radius: 5) [00:51:53 -78426.873782] SLOW spr round 7 (radius: 5) [00:52:53 -78426.057525] SLOW spr round 8 (radius: 5) [00:53:43 -78426.057308] SLOW spr round 9 (radius: 10) [00:54:31 -78426.057217] SLOW spr round 10 (radius: 15) [00:56:00 -78423.663189] SLOW spr round 11 (radius: 5) [00:57:08 -78423.633822] SLOW spr round 12 (radius: 10) [00:58:08 -78423.631783] SLOW spr round 13 (radius: 15) [00:59:30 -78423.631158] SLOW spr round 14 (radius: 20) [01:01:25 -78420.423579] SLOW spr round 15 (radius: 5) [01:02:36 -78420.422631] SLOW spr round 16 (radius: 10) [01:03:40 -78420.422477] SLOW spr round 17 (radius: 15) [01:05:03 -78420.422404] SLOW spr round 18 (radius: 20) [01:07:00 -78419.844395] SLOW spr round 19 (radius: 5) [01:08:10 -78419.841548] SLOW spr round 20 (radius: 10) [01:09:14 -78419.841139] SLOW spr round 21 (radius: 15) [01:10:35 -78419.840990] SLOW spr round 22 (radius: 20) [01:12:25 -78419.840915] SLOW spr round 23 (radius: 25) [01:14:37 -78419.840867] Model parameter optimization (eps = 0.100000) [01:14:44] ML tree search #2, logLikelihood: -78419.624648 [01:14:45 -325958.499077] Initial branch length optimization [01:14:46 -268793.029118] Model parameter optimization (eps = 10.000000) [01:15:24 -267022.441948] AUTODETECT spr round 1 (radius: 5) [01:15:58 -155359.648332] AUTODETECT spr round 2 (radius: 10) [01:16:38 -111103.780883] AUTODETECT spr round 3 (radius: 15) [01:17:27 -91549.282365] AUTODETECT spr round 4 (radius: 20) [01:18:26 -90330.977972] AUTODETECT spr round 5 (radius: 25) [01:19:30 -88877.628894] SPR radius for FAST iterations: 25 (autodetect) [01:19:30 -88877.628894] Model parameter optimization (eps = 3.000000) [01:19:50 -88481.803146] FAST spr round 1 (radius: 25) [01:20:40 -79140.198183] FAST spr round 2 (radius: 25) [01:21:17 -78538.783162] FAST spr round 3 (radius: 25) [01:21:52 -78509.201956] FAST spr round 4 (radius: 25) [01:22:21 -78506.795859] FAST spr round 5 (radius: 25) [01:22:48 -78506.795695] Model parameter optimization (eps = 1.000000) [01:23:03 -78498.727399] SLOW spr round 1 (radius: 5) [01:23:52 -78490.059825] SLOW spr round 2 (radius: 5) [01:24:37 -78490.031321] SLOW spr round 3 (radius: 10) [01:25:16 -78464.796205] SLOW spr round 4 (radius: 5) [01:26:23 -78426.279160] SLOW spr round 5 (radius: 5) [01:27:17 -78426.269154] SLOW spr round 6 (radius: 10) [01:28:08 -78424.714306] SLOW spr round 7 (radius: 5) [01:29:11 -78424.712762] SLOW spr round 8 (radius: 10) [01:30:06 -78424.712740] SLOW spr round 9 (radius: 15) [01:31:33 -78424.712718] SLOW spr round 10 (radius: 20) [01:33:33 -78424.712696] SLOW spr round 11 (radius: 25) [01:35:38 -78424.712675] Model parameter optimization (eps = 0.100000) [01:35:46] ML tree search #3, logLikelihood: -78424.578173 [01:35:46 -326262.310063] Initial branch length optimization [01:35:48 -267759.542862] Model parameter optimization (eps = 10.000000) [01:36:20 -265975.493700] AUTODETECT spr round 1 (radius: 5) [01:36:55 -154177.178643] AUTODETECT spr round 2 (radius: 10) [01:37:36 -105291.070013] AUTODETECT spr round 3 (radius: 15) [01:38:28 -89448.161437] AUTODETECT spr round 4 (radius: 20) [01:39:27 -87422.900816] AUTODETECT spr round 5 (radius: 25) [01:40:30 -86304.720011] SPR radius for FAST iterations: 25 (autodetect) [01:40:30 -86304.720011] Model parameter optimization (eps = 3.000000) [01:40:56 -85939.646333] FAST spr round 1 (radius: 25) [01:41:45 -79041.429915] FAST spr round 2 (radius: 25) [01:42:25 -78807.346837] FAST spr round 3 (radius: 25) [01:42:57 -78792.799306] FAST spr round 4 (radius: 25) [01:43:25 -78791.698022] FAST spr round 5 (radius: 25) [01:43:53 -78791.697898] Model parameter optimization (eps = 1.000000) [01:44:04 -78788.098475] SLOW spr round 1 (radius: 5) [01:44:54 -78775.054220] SLOW spr round 2 (radius: 5) [01:45:40 -78775.043602] SLOW spr round 3 (radius: 10) [01:46:26 -78773.900350] SLOW spr round 4 (radius: 5) [01:47:31 -78773.893462] SLOW spr round 5 (radius: 10) [01:48:27 -78773.136446] SLOW spr round 6 (radius: 5) [01:49:29 -78773.136384] SLOW spr round 7 (radius: 10) [01:50:23 -78773.136361] SLOW spr round 8 (radius: 15) [01:51:56 -78584.210146] SLOW spr round 9 (radius: 5) [01:53:09 -78419.160156] SLOW spr round 10 (radius: 5) [01:54:06 -78419.158840] SLOW spr round 11 (radius: 10) [01:54:57 -78419.158694] SLOW spr round 12 (radius: 15) [01:56:28 -78418.921919] SLOW spr round 13 (radius: 5) [01:57:36 -78418.916420] SLOW spr round 14 (radius: 10) [01:58:36 -78418.916206] SLOW spr round 15 (radius: 15) [02:00:07 -78418.916131] SLOW spr round 16 (radius: 20) [02:02:13 -78412.477668] SLOW spr round 17 (radius: 5) [02:03:23 -78412.477617] SLOW spr round 18 (radius: 10) [02:04:28 -78412.477611] SLOW spr round 19 (radius: 15) [02:05:57 -78412.477609] SLOW spr round 20 (radius: 20) [02:08:03 -78412.477608] SLOW spr round 21 (radius: 25) [02:10:17 -78412.477607] Model parameter optimization (eps = 0.100000) [02:10:25] ML tree search #4, logLikelihood: -78412.027479 [02:10:25 -323759.524069] Initial branch length optimization [02:10:27 -266278.617653] Model parameter optimization (eps = 10.000000) [02:11:04 -264580.571105] AUTODETECT spr round 1 (radius: 5) [02:11:23 -150528.048350] AUTODETECT spr round 2 (radius: 10) [02:11:50 -102622.705830] AUTODETECT spr round 3 (radius: 15) [02:12:42 -87946.903339] AUTODETECT spr round 4 (radius: 20) [02:13:50 -86573.893432] AUTODETECT spr round 5 (radius: 25) [02:15:03 -86464.022665] SPR radius for FAST iterations: 25 (autodetect) [02:15:03 -86464.022665] Model parameter optimization (eps = 3.000000) [02:15:24 -86050.851140] FAST spr round 1 (radius: 25) [02:16:11 -78754.037309] FAST spr round 2 (radius: 25) [02:16:46 -78493.643358] FAST spr round 3 (radius: 25) [02:17:19 -78484.495893] FAST spr round 4 (radius: 25) [02:17:48 -78481.888987] FAST spr round 5 (radius: 25) [02:18:17 -78477.747591] FAST spr round 6 (radius: 25) [02:18:46 -78473.053754] FAST spr round 7 (radius: 25) [02:19:14 -78473.053423] Model parameter optimization (eps = 1.000000) [02:19:25 -78467.476507] SLOW spr round 1 (radius: 5) [02:20:13 -78458.950053] SLOW spr round 2 (radius: 5) [02:20:59 -78457.934054] SLOW spr round 3 (radius: 5) [02:21:42 -78457.932594] SLOW spr round 4 (radius: 10) [02:22:32 -78419.864589] SLOW spr round 5 (radius: 5) [02:23:37 -78419.720994] SLOW spr round 6 (radius: 5) [02:24:29 -78419.719574] SLOW spr round 7 (radius: 10) [02:25:20 -78419.719095] SLOW spr round 8 (radius: 15) [02:26:54 -78382.081441] SLOW spr round 9 (radius: 5) [02:28:03 -78376.097550] SLOW spr round 10 (radius: 5) [02:29:01 -78374.621262] SLOW spr round 11 (radius: 5) [02:29:50 -78374.620265] SLOW spr round 12 (radius: 10) [02:30:38 -78374.620199] SLOW spr round 13 (radius: 15) [02:32:13 -78374.441283] SLOW spr round 14 (radius: 5) [02:33:22 -78374.411516] SLOW spr round 15 (radius: 10) [02:34:23 -78374.411193] SLOW spr round 16 (radius: 15) [02:35:54 -78374.411178] SLOW spr round 17 (radius: 20) [02:37:57 -78374.411167] SLOW spr round 18 (radius: 25) [02:40:11 -78374.411158] Model parameter optimization (eps = 0.100000) [02:40:17] ML tree search #5, logLikelihood: -78374.248854 [02:40:17 -322061.418878] Initial branch length optimization [02:40:19 -266217.820139] Model parameter optimization (eps = 10.000000) [02:40:56 -264402.663705] AUTODETECT spr round 1 (radius: 5) [02:41:29 -150289.463377] AUTODETECT spr round 2 (radius: 10) [02:42:08 -101086.118493] AUTODETECT spr round 3 (radius: 15) [02:42:57 -91408.733095] AUTODETECT spr round 4 (radius: 20) [02:43:54 -86908.945223] AUTODETECT spr round 5 (radius: 25) [02:44:56 -86481.391588] SPR radius for FAST iterations: 25 (autodetect) [02:44:56 -86481.391588] Model parameter optimization (eps = 3.000000) [02:45:22 -86143.661934] FAST spr round 1 (radius: 25) [02:46:08 -78885.553204] FAST spr round 2 (radius: 25) [02:46:49 -78554.432090] FAST spr round 3 (radius: 25) [02:47:19 -78541.348862] FAST spr round 4 (radius: 25) [02:47:50 -78537.572583] FAST spr round 5 (radius: 25) [02:48:18 -78537.572241] Model parameter optimization (eps = 1.000000) [02:48:28 -78534.866655] SLOW spr round 1 (radius: 5) [02:49:16 -78520.391373] SLOW spr round 2 (radius: 5) [02:50:05 -78517.484945] SLOW spr round 3 (radius: 5) [02:50:50 -78517.483492] SLOW spr round 4 (radius: 10) [02:51:36 -78510.140038] SLOW spr round 5 (radius: 5) [02:52:41 -78509.000470] SLOW spr round 6 (radius: 5) [02:53:34 -78509.000315] SLOW spr round 7 (radius: 10) [02:54:24 -78509.000281] SLOW spr round 8 (radius: 15) [02:55:52 -78497.077327] SLOW spr round 9 (radius: 5) [02:57:00 -78497.076502] SLOW spr round 10 (radius: 10) [02:58:01 -78496.703534] SLOW spr round 11 (radius: 5) [02:59:04 -78492.994100] SLOW spr round 12 (radius: 5) [02:59:57 -78492.991399] SLOW spr round 13 (radius: 10) [03:00:45 -78492.989716] SLOW spr round 14 (radius: 15) [03:02:13 -78492.988566] SLOW spr round 15 (radius: 20) [03:04:10 -78492.707482] SLOW spr round 16 (radius: 5) [03:05:21 -78491.966503] SLOW spr round 17 (radius: 5) [03:06:19 -78491.966108] SLOW spr round 18 (radius: 10) [03:07:11 -78491.965831] SLOW spr round 19 (radius: 15) [03:08:37 -78491.965634] SLOW spr round 20 (radius: 20) [03:10:34 -78491.965491] SLOW spr round 21 (radius: 25) [03:12:44 -78460.238617] SLOW spr round 22 (radius: 5) [03:13:56 -78431.790622] SLOW spr round 23 (radius: 5) [03:14:55 -78431.789007] SLOW spr round 24 (radius: 10) [03:15:45 -78431.788922] SLOW spr round 25 (radius: 15) [03:17:11 -78431.788894] SLOW spr round 26 (radius: 20) [03:19:10 -78431.788873] SLOW spr round 27 (radius: 25) [03:21:20 -78431.788855] Model parameter optimization (eps = 0.100000) [03:21:26] ML tree search #6, logLikelihood: -78431.696796 [03:21:26 -324786.453495] Initial branch length optimization [03:21:28 -264617.041414] Model parameter optimization (eps = 10.000000) [03:22:06 -263025.023150] AUTODETECT spr round 1 (radius: 5) [03:22:40 -154948.556584] AUTODETECT spr round 2 (radius: 10) [03:23:22 -113041.362554] AUTODETECT spr round 3 (radius: 15) [03:24:12 -94820.868314] AUTODETECT spr round 4 (radius: 20) [03:25:15 -87894.801288] AUTODETECT spr round 5 (radius: 25) [03:26:25 -87365.858859] SPR radius for FAST iterations: 25 (autodetect) [03:26:25 -87365.858859] Model parameter optimization (eps = 3.000000) [03:26:48 -86963.997793] FAST spr round 1 (radius: 25) [03:27:36 -78821.250557] FAST spr round 2 (radius: 25) [03:28:16 -78489.779060] FAST spr round 3 (radius: 25) [03:28:50 -78456.545647] FAST spr round 4 (radius: 25) [03:29:20 -78456.143044] FAST spr round 5 (radius: 25) [03:29:48 -78456.142835] Model parameter optimization (eps = 1.000000) [03:29:58 -78452.125472] SLOW spr round 1 (radius: 5) [03:30:47 -78435.072208] SLOW spr round 2 (radius: 5) [03:31:33 -78435.069911] SLOW spr round 3 (radius: 10) [03:32:20 -78435.069260] SLOW spr round 4 (radius: 15) [03:33:57 -78421.291934] SLOW spr round 5 (radius: 5) [03:35:07 -78412.673911] SLOW spr round 6 (radius: 5) [03:36:06 -78409.761729] SLOW spr round 7 (radius: 5) [03:36:55 -78409.761455] SLOW spr round 8 (radius: 10) [03:37:45 -78408.630268] SLOW spr round 9 (radius: 5) [03:38:48 -78408.623634] SLOW spr round 10 (radius: 10) [03:39:43 -78408.623560] SLOW spr round 11 (radius: 15) [03:41:13 -78408.623560] SLOW spr round 12 (radius: 20) [03:43:20 -78408.623559] SLOW spr round 13 (radius: 25) [03:45:36 -78408.623559] Model parameter optimization (eps = 0.100000) [03:45:41] ML tree search #7, logLikelihood: -78407.689748 [03:45:42 -324105.555863] Initial branch length optimization [03:45:44 -266221.727953] Model parameter optimization (eps = 10.000000) [03:46:21 -264532.122004] AUTODETECT spr round 1 (radius: 5) [03:46:55 -156774.902509] AUTODETECT spr round 2 (radius: 10) [03:47:36 -112592.189742] AUTODETECT spr round 3 (radius: 15) [03:48:24 -97073.108532] AUTODETECT spr round 4 (radius: 20) [03:49:00 -90815.075570] AUTODETECT spr round 5 (radius: 25) [03:50:03 -87779.583966] SPR radius for FAST iterations: 25 (autodetect) [03:50:03 -87779.583966] Model parameter optimization (eps = 3.000000) [03:50:28 -87323.830078] FAST spr round 1 (radius: 25) [03:51:14 -78832.935360] FAST spr round 2 (radius: 25) [03:51:50 -78536.501209] FAST spr round 3 (radius: 25) [03:52:24 -78509.840123] FAST spr round 4 (radius: 25) [03:52:56 -78499.486232] FAST spr round 5 (radius: 25) [03:53:25 -78499.483889] Model parameter optimization (eps = 1.000000) [03:53:39 -78493.635533] SLOW spr round 1 (radius: 5) [03:54:29 -78471.547581] SLOW spr round 2 (radius: 5) [03:55:15 -78471.546910] SLOW spr round 3 (radius: 10) [03:56:02 -78471.298812] SLOW spr round 4 (radius: 5) [03:56:39 -78471.046986] SLOW spr round 5 (radius: 5) [03:57:29 -78468.383023] SLOW spr round 6 (radius: 5) [03:58:17 -78468.382800] SLOW spr round 7 (radius: 10) [03:59:04 -78468.382795] SLOW spr round 8 (radius: 15) [04:00:31 -78468.382795] SLOW spr round 9 (radius: 20) [04:02:18 -78468.382795] SLOW spr round 10 (radius: 25) [04:04:19 -78443.827459] SLOW spr round 11 (radius: 5) [04:05:31 -78423.150331] SLOW spr round 12 (radius: 5) [04:06:31 -78423.150214] SLOW spr round 13 (radius: 10) [04:07:23 -78423.150206] SLOW spr round 14 (radius: 15) [04:08:48 -78423.150205] SLOW spr round 15 (radius: 20) [04:10:36 -78423.150205] SLOW spr round 16 (radius: 25) [04:12:36 -78423.150205] Model parameter optimization (eps = 0.100000) [04:12:40] ML tree search #8, logLikelihood: -78423.089339 [04:12:41 -326098.151851] Initial branch length optimization [04:12:42 -267824.208018] Model parameter optimization (eps = 10.000000) [04:13:03 -266185.045165] AUTODETECT spr round 1 (radius: 5) [04:13:35 -156537.828035] AUTODETECT spr round 2 (radius: 10) [04:14:19 -102271.868662] AUTODETECT spr round 3 (radius: 15) [04:15:09 -93914.308640] AUTODETECT spr round 4 (radius: 20) [04:16:11 -86681.804323] AUTODETECT spr round 5 (radius: 25) [04:17:19 -86248.568955] SPR radius for FAST iterations: 25 (autodetect) [04:17:19 -86248.568955] Model parameter optimization (eps = 3.000000) [04:17:42 -85851.979770] FAST spr round 1 (radius: 25) [04:18:30 -78863.799936] FAST spr round 2 (radius: 25) [04:19:12 -78541.570660] FAST spr round 3 (radius: 25) [04:19:47 -78499.757639] FAST spr round 4 (radius: 25) [04:20:18 -78493.450705] FAST spr round 5 (radius: 25) [04:20:49 -78490.378839] FAST spr round 6 (radius: 25) [04:21:17 -78490.377288] Model parameter optimization (eps = 1.000000) [04:21:30 -78481.649711] SLOW spr round 1 (radius: 5) [04:22:19 -78477.130208] SLOW spr round 2 (radius: 5) [04:23:06 -78477.122664] SLOW spr round 3 (radius: 10) [04:23:54 -78477.120666] SLOW spr round 4 (radius: 15) [04:25:24 -78474.272371] SLOW spr round 5 (radius: 5) [04:26:35 -78473.358557] SLOW spr round 6 (radius: 5) [04:27:33 -78473.358501] SLOW spr round 7 (radius: 10) [04:28:25 -78473.358473] SLOW spr round 8 (radius: 15) [04:29:51 -78473.358446] SLOW spr round 9 (radius: 20) [04:31:46 -78449.997624] SLOW spr round 10 (radius: 5) [04:32:59 -78442.083171] SLOW spr round 11 (radius: 5) [04:33:59 -78440.775670] SLOW spr round 12 (radius: 5) [04:34:51 -78440.775238] SLOW spr round 13 (radius: 10) [04:35:22 -78440.775178] SLOW spr round 14 (radius: 15) [04:36:11 -78440.775146] SLOW spr round 15 (radius: 20) [04:37:13 -78440.775118] SLOW spr round 16 (radius: 25) [04:38:22 -78440.775091] Model parameter optimization (eps = 0.100000) [04:38:25] ML tree search #9, logLikelihood: -78440.721275 [04:38:25 -327090.380641] Initial branch length optimization [04:38:26 -270441.209439] Model parameter optimization (eps = 10.000000) [04:38:46 -268800.430664] AUTODETECT spr round 1 (radius: 5) [04:39:05 -149153.652215] AUTODETECT spr round 2 (radius: 10) [04:39:28 -96871.789232] AUTODETECT spr round 3 (radius: 15) [04:39:54 -88615.780015] AUTODETECT spr round 4 (radius: 20) [04:40:31 -85568.643406] AUTODETECT spr round 5 (radius: 25) [04:41:10 -85441.488003] SPR radius for FAST iterations: 25 (autodetect) [04:41:10 -85441.488003] Model parameter optimization (eps = 3.000000) [04:41:22 -85028.719919] FAST spr round 1 (radius: 25) [04:41:50 -78714.637697] FAST spr round 2 (radius: 25) [04:42:12 -78503.239490] FAST spr round 3 (radius: 25) [04:42:31 -78475.423533] FAST spr round 4 (radius: 25) [04:42:47 -78475.398465] Model parameter optimization (eps = 1.000000) [04:42:55 -78472.116784] SLOW spr round 1 (radius: 5) [04:43:24 -78463.222900] SLOW spr round 2 (radius: 5) [04:43:51 -78463.222187] SLOW spr round 3 (radius: 10) [04:44:17 -78463.222163] SLOW spr round 4 (radius: 15) [04:45:07 -78463.222140] SLOW spr round 5 (radius: 20) [04:46:08 -78463.222117] SLOW spr round 6 (radius: 25) [04:47:14 -78463.222094] Model parameter optimization (eps = 0.100000) [04:47:16] ML tree search #10, logLikelihood: -78463.200702 [04:47:16 -319547.667604] Initial branch length optimization [04:47:17 -261995.415461] Model parameter optimization (eps = 10.000000) [04:47:35 -260242.887100] AUTODETECT spr round 1 (radius: 5) [04:47:53 -151184.075076] AUTODETECT spr round 2 (radius: 10) [04:48:14 -107982.296824] AUTODETECT spr round 3 (radius: 15) [04:48:43 -93625.399185] AUTODETECT spr round 4 (radius: 20) [04:49:14 -89063.309181] AUTODETECT spr round 5 (radius: 25) [04:49:42 -88934.975104] SPR radius for FAST iterations: 25 (autodetect) [04:49:42 -88934.975104] Model parameter optimization (eps = 3.000000) [04:49:53 -88555.270358] FAST spr round 1 (radius: 25) [04:50:18 -78967.889717] FAST spr round 2 (radius: 25) [04:50:41 -78510.393857] FAST spr round 3 (radius: 25) [04:50:59 -78502.190263] FAST spr round 4 (radius: 25) [04:51:15 -78502.187150] Model parameter optimization (eps = 1.000000) [04:51:21 -78495.493307] SLOW spr round 1 (radius: 5) [04:51:48 -78475.639842] SLOW spr round 2 (radius: 5) [04:52:14 -78475.443332] SLOW spr round 3 (radius: 5) [04:52:38 -78475.442510] SLOW spr round 4 (radius: 10) [04:53:04 -78475.442414] SLOW spr round 5 (radius: 15) [04:53:57 -78445.331097] SLOW spr round 6 (radius: 5) [04:54:36 -78423.597977] SLOW spr round 7 (radius: 5) [04:55:08 -78423.597046] SLOW spr round 8 (radius: 10) [04:55:37 -78423.597015] SLOW spr round 9 (radius: 15) [04:56:26 -78423.597011] SLOW spr round 10 (radius: 20) [04:57:33 -78423.597010] SLOW spr round 11 (radius: 25) [04:58:48 -78423.597009] Model parameter optimization (eps = 0.100000) [04:58:53] ML tree search #11, logLikelihood: -78423.081321 [04:58:53 -325458.636850] Initial branch length optimization [04:58:54 -266997.413535] Model parameter optimization (eps = 10.000000) [04:59:16 -265311.590058] AUTODETECT spr round 1 (radius: 5) [04:59:34 -148359.460961] AUTODETECT spr round 2 (radius: 10) [04:59:55 -104730.568736] AUTODETECT spr round 3 (radius: 15) [05:00:25 -87812.762133] AUTODETECT spr round 4 (radius: 20) [05:00:55 -86518.776908] AUTODETECT spr round 5 (radius: 25) [05:01:29 -85602.224863] SPR radius for FAST iterations: 25 (autodetect) [05:01:29 -85602.224863] Model parameter optimization (eps = 3.000000) [05:01:41 -85214.866938] FAST spr round 1 (radius: 25) [05:02:07 -78946.057633] FAST spr round 2 (radius: 25) [05:02:29 -78568.298040] FAST spr round 3 (radius: 25) [05:02:46 -78510.023448] FAST spr round 4 (radius: 25) [05:03:02 -78509.412208] FAST spr round 5 (radius: 25) [05:03:18 -78509.411699] Model parameter optimization (eps = 1.000000) [05:03:25 -78506.585683] SLOW spr round 1 (radius: 5) [05:03:53 -78495.160780] SLOW spr round 2 (radius: 5) [05:04:19 -78494.300904] SLOW spr round 3 (radius: 5) [05:04:44 -78493.826092] SLOW spr round 4 (radius: 5) [05:05:08 -78493.825999] SLOW spr round 5 (radius: 10) [05:05:35 -78489.747230] SLOW spr round 6 (radius: 5) [05:06:13 -78450.209037] SLOW spr round 7 (radius: 5) [05:06:44 -78447.075727] SLOW spr round 8 (radius: 5) [05:07:11 -78447.029034] SLOW spr round 9 (radius: 10) [05:07:39 -78444.648600] SLOW spr round 10 (radius: 5) [05:08:15 -78444.647543] SLOW spr round 11 (radius: 10) [05:08:47 -78444.489497] SLOW spr round 12 (radius: 5) [05:09:22 -78444.489163] SLOW spr round 13 (radius: 10) [05:09:53 -78444.488921] SLOW spr round 14 (radius: 15) [05:10:43 -78444.057952] SLOW spr round 15 (radius: 5) [05:11:23 -78442.160398] SLOW spr round 16 (radius: 5) [05:11:55 -78437.801501] SLOW spr round 17 (radius: 5) [05:12:23 -78437.801433] SLOW spr round 18 (radius: 10) [05:12:51 -78437.801377] SLOW spr round 19 (radius: 15) [05:13:42 -78437.801329] SLOW spr round 20 (radius: 20) [05:14:51 -78437.801287] SLOW spr round 21 (radius: 25) [05:16:07 -78437.801249] Model parameter optimization (eps = 0.100000) [05:16:12] ML tree search #12, logLikelihood: -78437.504928 [05:16:12 -323591.535101] Initial branch length optimization [05:16:13 -265044.182999] Model parameter optimization (eps = 10.000000) [05:16:35 -263333.081820] AUTODETECT spr round 1 (radius: 5) [05:16:54 -158502.315439] AUTODETECT spr round 2 (radius: 10) [05:17:16 -102077.101492] AUTODETECT spr round 3 (radius: 15) [05:17:42 -90899.997137] AUTODETECT spr round 4 (radius: 20) [05:18:19 -87855.812184] AUTODETECT spr round 5 (radius: 25) [05:19:00 -87150.467224] SPR radius for FAST iterations: 25 (autodetect) [05:19:00 -87150.467224] Model parameter optimization (eps = 3.000000) [05:19:12 -86782.068701] FAST spr round 1 (radius: 25) [05:19:37 -78808.435899] FAST spr round 2 (radius: 25) [05:19:58 -78444.046220] FAST spr round 3 (radius: 25) [05:20:17 -78414.958352] FAST spr round 4 (radius: 25) [05:20:34 -78412.529087] FAST spr round 5 (radius: 25) [05:20:49 -78412.528998] Model parameter optimization (eps = 1.000000) [05:20:55 -78409.453406] SLOW spr round 1 (radius: 5) [05:21:23 -78391.811484] SLOW spr round 2 (radius: 5) [05:21:50 -78391.794963] SLOW spr round 3 (radius: 10) [05:22:17 -78391.132003] SLOW spr round 4 (radius: 5) [05:22:54 -78391.131963] SLOW spr round 5 (radius: 10) [05:23:27 -78390.904037] SLOW spr round 6 (radius: 5) [05:24:03 -78390.648501] SLOW spr round 7 (radius: 5) [05:24:33 -78389.336997] SLOW spr round 8 (radius: 5) [05:25:00 -78389.336558] SLOW spr round 9 (radius: 10) [05:25:27 -78389.092562] SLOW spr round 10 (radius: 5) [05:26:04 -78385.686638] SLOW spr round 11 (radius: 5) [05:26:34 -78385.684979] SLOW spr round 12 (radius: 10) [05:27:02 -78385.683855] SLOW spr round 13 (radius: 15) [05:27:57 -78380.463545] SLOW spr round 14 (radius: 5) [05:28:37 -78380.434782] SLOW spr round 15 (radius: 10) [05:29:12 -78380.434458] SLOW spr round 16 (radius: 15) [05:30:05 -78380.434378] SLOW spr round 17 (radius: 20) [05:31:16 -78380.434324] SLOW spr round 18 (radius: 25) [05:32:36 -78380.434285] Model parameter optimization (eps = 0.100000) [05:32:41] ML tree search #13, logLikelihood: -78380.189881 [05:32:41 -328970.329155] Initial branch length optimization [05:32:42 -272281.355326] Model parameter optimization (eps = 10.000000) [05:33:01 -270621.203381] AUTODETECT spr round 1 (radius: 5) [05:33:20 -157722.395034] AUTODETECT spr round 2 (radius: 10) [05:33:43 -99210.706438] AUTODETECT spr round 3 (radius: 15) [05:34:12 -85740.568145] AUTODETECT spr round 4 (radius: 20) [05:34:43 -85165.090656] AUTODETECT spr round 5 (radius: 25) [05:35:20 -85123.651206] SPR radius for FAST iterations: 25 (autodetect) [05:35:20 -85123.651206] Model parameter optimization (eps = 3.000000) [05:35:32 -84759.643250] FAST spr round 1 (radius: 25) [05:35:58 -78745.689978] FAST spr round 2 (radius: 25) [05:36:19 -78494.132476] FAST spr round 3 (radius: 25) [05:36:37 -78482.948229] FAST spr round 4 (radius: 25) [05:36:54 -78481.251850] FAST spr round 5 (radius: 25) [05:37:10 -78481.250230] Model parameter optimization (eps = 1.000000) [05:37:16 -78475.907122] SLOW spr round 1 (radius: 5) [05:37:44 -78468.705563] SLOW spr round 2 (radius: 5) [05:38:11 -78467.901959] SLOW spr round 3 (radius: 5) [05:38:37 -78467.901904] SLOW spr round 4 (radius: 10) [05:39:03 -78467.901891] SLOW spr round 5 (radius: 15) [05:39:54 -78432.895457] SLOW spr round 6 (radius: 5) [05:40:33 -78429.359801] SLOW spr round 7 (radius: 5) [05:41:05 -78429.359525] SLOW spr round 8 (radius: 10) [05:41:34 -78429.359462] SLOW spr round 9 (radius: 15) [05:42:22 -78429.359445] SLOW spr round 10 (radius: 20) [05:43:29 -78427.249420] SLOW spr round 11 (radius: 5) [05:44:09 -78425.837343] SLOW spr round 12 (radius: 5) [05:44:42 -78425.837030] SLOW spr round 13 (radius: 10) [05:45:11 -78425.730314] SLOW spr round 14 (radius: 5) [05:45:46 -78422.302322] SLOW spr round 15 (radius: 5) [05:46:16 -78422.302080] SLOW spr round 16 (radius: 10) [05:46:44 -78422.302076] SLOW spr round 17 (radius: 15) [05:47:32 -78422.302074] SLOW spr round 18 (radius: 20) [05:48:37 -78422.302074] SLOW spr round 19 (radius: 25) [05:49:52 -78422.302074] Model parameter optimization (eps = 0.100000) [05:49:56] ML tree search #14, logLikelihood: -78422.079316 [05:49:56 -330142.061809] Initial branch length optimization [05:49:57 -274220.932278] Model parameter optimization (eps = 10.000000) [05:50:16 -272415.140553] AUTODETECT spr round 1 (radius: 5) [05:50:34 -151454.925741] AUTODETECT spr round 2 (radius: 10) [05:50:57 -105716.050600] AUTODETECT spr round 3 (radius: 15) [05:51:25 -87993.251041] AUTODETECT spr round 4 (radius: 20) [05:51:59 -86734.237811] AUTODETECT spr round 5 (radius: 25) [05:52:36 -86734.230660] SPR radius for FAST iterations: 20 (autodetect) [05:52:36 -86734.230660] Model parameter optimization (eps = 3.000000) [05:52:47 -86295.996373] FAST spr round 1 (radius: 20) [05:53:13 -79334.715643] FAST spr round 2 (radius: 20) [05:53:32 -78543.514811] FAST spr round 3 (radius: 20) [05:53:50 -78417.995564] FAST spr round 4 (radius: 20) [05:54:06 -78417.993726] Model parameter optimization (eps = 1.000000) [05:54:14 -78411.390653] SLOW spr round 1 (radius: 5) [05:54:40 -78397.332665] SLOW spr round 2 (radius: 5) [05:55:06 -78396.728811] SLOW spr round 3 (radius: 5) [05:55:31 -78396.728608] SLOW spr round 4 (radius: 10) [05:55:57 -78381.650836] SLOW spr round 5 (radius: 5) [05:56:33 -78381.646618] SLOW spr round 6 (radius: 10) [05:57:05 -78381.645750] SLOW spr round 7 (radius: 15) [05:57:54 -78381.476788] SLOW spr round 8 (radius: 5) [05:58:33 -78381.381028] SLOW spr round 9 (radius: 10) [05:59:06 -78381.380903] SLOW spr round 10 (radius: 15) [05:59:56 -78381.380841] SLOW spr round 11 (radius: 20) [06:01:03 -78381.380798] SLOW spr round 12 (radius: 25) [06:02:14 -78381.380762] Model parameter optimization (eps = 0.100000) [06:02:20] ML tree search #15, logLikelihood: -78381.154753 [06:02:20 -326182.068994] Initial branch length optimization [06:02:21 -271453.448263] Model parameter optimization (eps = 10.000000) [06:02:37 -269760.699957] AUTODETECT spr round 1 (radius: 5) [06:02:56 -161091.798257] AUTODETECT spr round 2 (radius: 10) [06:03:19 -106154.085130] AUTODETECT spr round 3 (radius: 15) [06:03:46 -88778.169119] AUTODETECT spr round 4 (radius: 20) [06:04:20 -86441.755351] AUTODETECT spr round 5 (radius: 25) [06:04:55 -86434.913426] SPR radius for FAST iterations: 25 (autodetect) [06:04:55 -86434.913426] Model parameter optimization (eps = 3.000000) [06:05:08 -86024.598833] FAST spr round 1 (radius: 25) [06:05:34 -78970.341247] FAST spr round 2 (radius: 25) [06:05:57 -78487.167958] FAST spr round 3 (radius: 25) [06:06:16 -78459.573315] FAST spr round 4 (radius: 25) [06:06:32 -78456.345164] FAST spr round 5 (radius: 25) [06:06:48 -78456.343931] Model parameter optimization (eps = 1.000000) [06:06:53 -78452.805065] SLOW spr round 1 (radius: 5) [06:07:21 -78439.161333] SLOW spr round 2 (radius: 5) [06:07:47 -78424.084601] SLOW spr round 3 (radius: 5) [06:08:12 -78424.002398] SLOW spr round 4 (radius: 10) [06:08:39 -78422.759244] SLOW spr round 5 (radius: 5) [06:09:15 -78389.874991] SLOW spr round 6 (radius: 5) [06:09:46 -78386.774770] SLOW spr round 7 (radius: 5) [06:10:13 -78386.616326] SLOW spr round 8 (radius: 5) [06:10:39 -78386.616144] SLOW spr round 9 (radius: 10) [06:11:05 -78386.616128] SLOW spr round 10 (radius: 15) [06:11:58 -78386.616115] SLOW spr round 11 (radius: 20) [06:13:03 -78386.616103] SLOW spr round 12 (radius: 25) [06:14:11 -78386.616091] Model parameter optimization (eps = 0.100000) [06:14:16] ML tree search #16, logLikelihood: -78386.507837 [06:14:16 -327419.076245] Initial branch length optimization [06:14:17 -266847.158843] Model parameter optimization (eps = 10.000000) [06:14:35 -265187.226647] AUTODETECT spr round 1 (radius: 5) [06:14:54 -158692.354741] AUTODETECT spr round 2 (radius: 10) [06:15:16 -114656.630690] AUTODETECT spr round 3 (radius: 15) [06:15:43 -92433.870099] AUTODETECT spr round 4 (radius: 20) [06:16:14 -86611.042696] AUTODETECT spr round 5 (radius: 25) [06:16:43 -86120.373436] SPR radius for FAST iterations: 25 (autodetect) [06:16:43 -86120.373436] Model parameter optimization (eps = 3.000000) [06:16:56 -85756.121401] FAST spr round 1 (radius: 25) [06:17:21 -79181.519937] FAST spr round 2 (radius: 25) [06:17:43 -78582.831634] FAST spr round 3 (radius: 25) [06:18:03 -78519.188351] FAST spr round 4 (radius: 25) [06:18:20 -78495.975722] FAST spr round 5 (radius: 25) [06:18:36 -78489.834675] FAST spr round 6 (radius: 25) [06:18:52 -78489.834366] Model parameter optimization (eps = 1.000000) [06:18:58 -78482.663901] SLOW spr round 1 (radius: 5) [06:19:25 -78458.754044] SLOW spr round 2 (radius: 5) [06:19:50 -78456.553664] SLOW spr round 3 (radius: 5) [06:20:15 -78456.551276] SLOW spr round 4 (radius: 10) [06:20:42 -78455.139227] SLOW spr round 5 (radius: 5) [06:21:17 -78455.139118] SLOW spr round 6 (radius: 10) [06:21:48 -78455.139098] SLOW spr round 7 (radius: 15) [06:22:36 -78455.139086] SLOW spr round 8 (radius: 20) [06:23:41 -78455.139077] SLOW spr round 9 (radius: 25) [06:24:57 -78415.210012] SLOW spr round 10 (radius: 5) [06:25:37 -78414.435770] SLOW spr round 11 (radius: 5) [06:26:10 -78414.435347] SLOW spr round 12 (radius: 10) [06:26:39 -78414.435278] SLOW spr round 13 (radius: 15) [06:27:27 -78414.435260] SLOW spr round 14 (radius: 20) [06:28:34 -78409.370433] SLOW spr round 15 (radius: 5) [06:29:13 -78409.370395] SLOW spr round 16 (radius: 10) [06:29:49 -78409.370382] SLOW spr round 17 (radius: 15) [06:30:37 -78409.370373] SLOW spr round 18 (radius: 20) [06:31:43 -78409.370365] SLOW spr round 19 (radius: 25) [06:32:59 -78408.976985] SLOW spr round 20 (radius: 5) [06:33:39 -78408.947975] SLOW spr round 21 (radius: 10) [06:34:14 -78408.947762] SLOW spr round 22 (radius: 15) [06:35:01 -78408.947750] SLOW spr round 23 (radius: 20) [06:36:08 -78408.823334] SLOW spr round 24 (radius: 5) [06:36:47 -78408.823113] SLOW spr round 25 (radius: 10) [06:37:23 -78408.823100] SLOW spr round 26 (radius: 15) [06:38:10 -78408.823091] SLOW spr round 27 (radius: 20) [06:39:16 -78408.823083] SLOW spr round 28 (radius: 25) [06:40:32 -78408.823075] Model parameter optimization (eps = 0.100000) [06:40:35] ML tree search #17, logLikelihood: -78408.657058 [06:40:35 -328555.511226] Initial branch length optimization [06:40:37 -270580.617671] Model parameter optimization (eps = 10.000000) [06:40:56 -268744.711300] AUTODETECT spr round 1 (radius: 5) [06:41:14 -156053.763034] AUTODETECT spr round 2 (radius: 10) [06:41:37 -105800.145396] AUTODETECT spr round 3 (radius: 15) [06:42:02 -92312.815580] AUTODETECT spr round 4 (radius: 20) [06:42:30 -87473.401381] AUTODETECT spr round 5 (radius: 25) [06:43:07 -86788.965154] SPR radius for FAST iterations: 25 (autodetect) [06:43:07 -86788.965154] Model parameter optimization (eps = 3.000000) [06:43:20 -86468.681521] FAST spr round 1 (radius: 25) [06:43:43 -78641.389617] FAST spr round 2 (radius: 25) [06:44:02 -78432.859380] FAST spr round 3 (radius: 25) [06:44:19 -78418.689140] FAST spr round 4 (radius: 25) [06:44:35 -78418.687423] Model parameter optimization (eps = 1.000000) [06:44:43 -78415.412226] SLOW spr round 1 (radius: 5) [06:45:09 -78398.178118] SLOW spr round 2 (radius: 5) [06:45:36 -78396.168777] SLOW spr round 3 (radius: 5) [06:46:01 -78396.168652] SLOW spr round 4 (radius: 10) [06:46:28 -78396.168611] SLOW spr round 5 (radius: 15) [06:47:21 -78395.946065] SLOW spr round 6 (radius: 5) [06:48:01 -78393.585234] SLOW spr round 7 (radius: 5) [06:48:35 -78392.466162] SLOW spr round 8 (radius: 5) [06:49:03 -78392.465700] SLOW spr round 9 (radius: 10) [06:49:30 -78392.465510] SLOW spr round 10 (radius: 15) [06:50:22 -78392.465430] SLOW spr round 11 (radius: 20) [06:51:30 -78392.465389] SLOW spr round 12 (radius: 25) [06:52:48 -78392.465360] Model parameter optimization (eps = 0.100000) [06:52:52] ML tree search #18, logLikelihood: -78392.328637 [06:52:52 -325507.163795] Initial branch length optimization [06:52:53 -266618.001937] Model parameter optimization (eps = 10.000000) [06:53:12 -264979.413361] AUTODETECT spr round 1 (radius: 5) [06:53:31 -152999.966606] AUTODETECT spr round 2 (radius: 10) [06:53:53 -110136.919550] AUTODETECT spr round 3 (radius: 15) [06:54:22 -91271.087152] AUTODETECT spr round 4 (radius: 20) [06:54:54 -88211.877094] AUTODETECT spr round 5 (radius: 25) [06:55:27 -87598.817400] SPR radius for FAST iterations: 25 (autodetect) [06:55:27 -87598.817400] Model parameter optimization (eps = 3.000000) [06:55:42 -87169.721497] FAST spr round 1 (radius: 25) [06:56:08 -78740.953953] FAST spr round 2 (radius: 25) [06:56:30 -78511.446424] FAST spr round 3 (radius: 25) [06:56:48 -78510.139983] FAST spr round 4 (radius: 25) [06:57:05 -78509.519307] FAST spr round 5 (radius: 25) [06:57:21 -78509.518250] Model parameter optimization (eps = 1.000000) [06:57:28 -78505.169495] SLOW spr round 1 (radius: 5) [06:57:56 -78485.879538] SLOW spr round 2 (radius: 5) [06:58:21 -78485.877521] SLOW spr round 3 (radius: 10) [06:58:47 -78485.473828] SLOW spr round 4 (radius: 5) [06:59:29 -78434.722843] SLOW spr round 5 (radius: 5) [07:00:00 -78434.142525] SLOW spr round 6 (radius: 5) [07:00:28 -78434.142358] SLOW spr round 7 (radius: 10) [07:00:55 -78433.135049] SLOW spr round 8 (radius: 5) [07:01:32 -78433.133576] SLOW spr round 9 (radius: 10) [07:02:05 -78433.133576] SLOW spr round 10 (radius: 15) [07:02:56 -78370.683878] SLOW spr round 11 (radius: 5) [07:03:36 -78370.683751] SLOW spr round 12 (radius: 10) [07:04:11 -78370.683728] SLOW spr round 13 (radius: 15) [07:05:01 -78370.683720] SLOW spr round 14 (radius: 20) [07:06:08 -78370.683717] SLOW spr round 15 (radius: 25) [07:07:22 -78370.683716] Model parameter optimization (eps = 0.100000) [07:07:27] ML tree search #19, logLikelihood: -78370.525506 [07:07:27 -323188.233755] Initial branch length optimization [07:07:28 -267823.511496] Model parameter optimization (eps = 10.000000) [07:07:50 -266077.258599] AUTODETECT spr round 1 (radius: 5) [07:08:08 -156388.256110] AUTODETECT spr round 2 (radius: 10) [07:08:31 -102336.144703] AUTODETECT spr round 3 (radius: 15) [07:08:58 -85774.617478] AUTODETECT spr round 4 (radius: 20) [07:09:28 -84591.699350] AUTODETECT spr round 5 (radius: 25) [07:09:58 -84364.596811] SPR radius for FAST iterations: 25 (autodetect) [07:09:58 -84364.596811] Model parameter optimization (eps = 3.000000) [07:10:12 -83999.714344] FAST spr round 1 (radius: 25) [07:10:36 -78787.267056] FAST spr round 2 (radius: 25) [07:10:57 -78553.467394] FAST spr round 3 (radius: 25) [07:11:16 -78517.029633] FAST spr round 4 (radius: 25) [07:11:32 -78517.029353] Model parameter optimization (eps = 1.000000) [07:11:39 -78512.277105] SLOW spr round 1 (radius: 5) [07:12:07 -78499.521209] SLOW spr round 2 (radius: 5) [07:12:33 -78498.907531] SLOW spr round 3 (radius: 5) [07:12:59 -78498.464004] SLOW spr round 4 (radius: 5) [07:13:25 -78498.047662] SLOW spr round 5 (radius: 5) [07:13:51 -78498.046988] SLOW spr round 6 (radius: 10) [07:14:19 -78494.088584] SLOW spr round 7 (radius: 5) [07:14:56 -78494.088256] SLOW spr round 8 (radius: 10) [07:15:27 -78493.434484] SLOW spr round 9 (radius: 5) [07:16:02 -78493.434379] SLOW spr round 10 (radius: 10) [07:16:33 -78493.434313] SLOW spr round 11 (radius: 15) [07:17:22 -78493.434266] SLOW spr round 12 (radius: 20) [07:18:25 -78430.790284] SLOW spr round 13 (radius: 5) [07:19:05 -78430.790149] SLOW spr round 14 (radius: 10) [07:19:41 -78430.790118] SLOW spr round 15 (radius: 15) [07:20:29 -78430.790101] SLOW spr round 16 (radius: 20) [07:21:34 -78430.790090] SLOW spr round 17 (radius: 25) [07:22:49 -78430.790083] Model parameter optimization (eps = 0.100000) [07:22:54] ML tree search #20, logLikelihood: -78430.660817 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.157977,0.580272) (0.069097,1.382850) (0.415428,0.725444) (0.357498,1.430525) 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: -78370.525506 AIC score: 158191.051012 / AICc score: 165071.443169 / BIC score: 161655.670063 Free parameters (model + branch lengths): 725 WARNING: Best ML tree contains 58 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q02297/3_mltree/Q02297.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q02297/3_mltree/Q02297.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q02297/3_mltree/Q02297.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q02297/3_mltree/Q02297.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q02297/3_mltree/Q02297.raxml.log Analysis started: 13-Jul-2021 16:15:04 / finished: 13-Jul-2021 23:37:58 Elapsed time: 26574.517 seconds Consumed energy: 2473.470 Wh (= 12 km in an electric car, or 62 km with an e-scooter!)