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 17:32:17 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A8TX70/2_msa/A8TX70_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A8TX70/3_mltree/A8TX70 --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/A8TX70/2_msa/A8TX70_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 899 sites WARNING: Sequences tr_H2R8V5_H2R8V5_PANTR_9598 and tr_A0A2R9BC08_A0A2R9BC08_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7C8P4_K7C8P4_PANTR_9598 and tr_A0A2R8ZQ62_A0A2R8ZQ62_PANPA_9597 are exactly identical! WARNING: Sequences tr_B5AYU5_B5AYU5_CAVPO_10141 and sp_P84552_COCH_CAVPO_10141 are exactly identical! WARNING: Sequences tr_G1LJ22_G1LJ22_AILME_9646 and tr_A0A384C518_A0A384C518_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2D0QP39_A0A2D0QP39_ICTPU_7998 and tr_A0A2D0QQS3_A0A2D0QQS3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5MHL6_A0A2K5MHL6_CERAT_9531 and tr_A0A2K5Y4B3_A0A2K5Y4B3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5NK39_A0A2K5NK39_CERAT_9531 and tr_A0A2K6CKR7_A0A2K6CKR7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K5P5K0_A0A2K5P5K0_CERAT_9531 and tr_A0A2K5ZDS6_A0A2K5ZDS6_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K6DZZ4_A0A2K6DZZ4_MACNE_9545 and tr_A0A2K5YRS9_A0A2K5YRS9_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 9 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/A8TX70/3_mltree/A8TX70.raxml.reduced.phy Alignment comprises 1 partitions and 899 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 899 / 899 Gaps: 31.51 % Invariant sites: 0.11 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A8TX70/3_mltree/A8TX70.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 / 100 / 8000 [00:00:00] Data distribution: max. searches per worker: 20 Starting ML tree search with 20 distinct starting trees [00:00:00 -1371657.948463] Initial branch length optimization [00:00:05 -1158631.145638] Model parameter optimization (eps = 10.000000) [00:00:35 -1157269.124949] AUTODETECT spr round 1 (radius: 5) [00:02:26 -820798.783727] AUTODETECT spr round 2 (radius: 10) [00:04:42 -609142.991145] AUTODETECT spr round 3 (radius: 15) [00:06:48 -528774.215500] AUTODETECT spr round 4 (radius: 20) [00:09:25 -502495.914809] AUTODETECT spr round 5 (radius: 25) [00:12:19 -475607.730273] SPR radius for FAST iterations: 25 (autodetect) [00:12:19 -475607.730273] Model parameter optimization (eps = 3.000000) [00:12:38 -474874.679667] FAST spr round 1 (radius: 25) [00:15:33 -417746.798110] FAST spr round 2 (radius: 25) [00:17:42 -414678.140494] FAST spr round 3 (radius: 25) [00:19:33 -414545.678017] FAST spr round 4 (radius: 25) [00:21:16 -414490.856735] FAST spr round 5 (radius: 25) [00:22:48 -414490.806662] Model parameter optimization (eps = 1.000000) [00:23:05 -414456.456610] SLOW spr round 1 (radius: 5) [00:25:09 -414367.501030] SLOW spr round 2 (radius: 5) [00:27:09 -414362.581788] SLOW spr round 3 (radius: 5) [00:29:05 -414362.581671] SLOW spr round 4 (radius: 10) [00:31:12 -414341.288462] SLOW spr round 5 (radius: 5) [00:33:34 -414323.921704] SLOW spr round 6 (radius: 5) [00:35:41 -414321.294819] SLOW spr round 7 (radius: 5) [00:37:39 -414321.294540] SLOW spr round 8 (radius: 10) [00:39:44 -414321.073851] SLOW spr round 9 (radius: 5) [00:42:01 -414321.073658] SLOW spr round 10 (radius: 10) [00:44:22 -414321.073636] SLOW spr round 11 (radius: 15) [00:47:53 -414321.073629] SLOW spr round 12 (radius: 20) [00:53:17 -414321.073627] SLOW spr round 13 (radius: 25) [01:00:21 -414321.073625] Model parameter optimization (eps = 0.100000) [01:00:29] ML tree search #1, logLikelihood: -414320.761024 [01:00:29 -1374506.553425] Initial branch length optimization [01:00:34 -1160529.971081] Model parameter optimization (eps = 10.000000) [01:00:57 -1159181.618914] AUTODETECT spr round 1 (radius: 5) [01:02:50 -824717.620563] AUTODETECT spr round 2 (radius: 10) [01:05:03 -605767.564047] AUTODETECT spr round 3 (radius: 15) [01:07:11 -531912.446760] AUTODETECT spr round 4 (radius: 20) [01:09:54 -498083.422078] AUTODETECT spr round 5 (radius: 25) [01:13:00 -477407.283676] SPR radius for FAST iterations: 25 (autodetect) [01:13:00 -477407.283676] Model parameter optimization (eps = 3.000000) [01:13:07 -477393.109147] FAST spr round 1 (radius: 25) [01:16:07 -417829.841913] FAST spr round 2 (radius: 25) [01:18:20 -415494.635484] FAST spr round 3 (radius: 25) [01:20:19 -415319.555076] FAST spr round 4 (radius: 25) [01:22:01 -415305.088526] FAST spr round 5 (radius: 25) [01:23:35 -415301.027292] FAST spr round 6 (radius: 25) [01:25:07 -415297.688393] FAST spr round 7 (radius: 25) [01:26:42 -415293.934913] FAST spr round 8 (radius: 25) [01:28:09 -415293.933817] Model parameter optimization (eps = 1.000000) [01:28:46 -414480.051375] SLOW spr round 1 (radius: 5) [01:30:48 -414349.410860] SLOW spr round 2 (radius: 5) [01:32:49 -414328.367251] SLOW spr round 3 (radius: 5) [01:34:40 -414328.280054] SLOW spr round 4 (radius: 10) [01:36:42 -414312.912947] SLOW spr round 5 (radius: 5) [01:39:01 -414299.219035] SLOW spr round 6 (radius: 5) [01:41:04 -414298.659897] SLOW spr round 7 (radius: 5) [01:43:00 -414298.651082] SLOW spr round 8 (radius: 10) [01:45:07 -414298.650797] SLOW spr round 9 (radius: 15) [01:48:55 -414298.650768] SLOW spr round 10 (radius: 20) [01:54:29 -414298.650764] SLOW spr round 11 (radius: 25) [02:01:58 -414298.650764] Model parameter optimization (eps = 0.100000) [02:02:08] ML tree search #2, logLikelihood: -414298.303057 [02:02:09 -1377807.676713] Initial branch length optimization [02:02:13 -1159190.343035] Model parameter optimization (eps = 10.000000) [02:02:40 -1157786.985987] AUTODETECT spr round 1 (radius: 5) [02:04:34 -820765.748597] AUTODETECT spr round 2 (radius: 10) [02:06:57 -600541.419773] AUTODETECT spr round 3 (radius: 15) [02:09:03 -531304.569233] AUTODETECT spr round 4 (radius: 20) [02:11:39 -480017.461675] AUTODETECT spr round 5 (radius: 25) [02:14:45 -467657.319645] SPR radius for FAST iterations: 25 (autodetect) [02:14:45 -467657.319645] Model parameter optimization (eps = 3.000000) [02:15:17 -466728.489786] FAST spr round 1 (radius: 25) [02:18:06 -416441.240687] FAST spr round 2 (radius: 25) [02:20:18 -414573.598609] FAST spr round 3 (radius: 25) [02:22:13 -414455.020605] FAST spr round 4 (radius: 25) [02:23:49 -414442.221240] FAST spr round 5 (radius: 25) [02:25:22 -414441.635766] FAST spr round 6 (radius: 25) [02:26:55 -414441.623981] Model parameter optimization (eps = 1.000000) [02:27:12 -414433.453616] SLOW spr round 1 (radius: 5) [02:29:18 -414348.716596] SLOW spr round 2 (radius: 5) [02:31:21 -414341.774906] SLOW spr round 3 (radius: 5) [02:33:12 -414341.770388] SLOW spr round 4 (radius: 10) [02:35:17 -414339.806519] SLOW spr round 5 (radius: 5) [02:37:41 -414337.829327] SLOW spr round 6 (radius: 5) [02:39:45 -414335.114055] SLOW spr round 7 (radius: 5) [02:41:51 -414335.108457] SLOW spr round 8 (radius: 10) [02:43:54 -414334.991964] SLOW spr round 9 (radius: 5) [02:46:15 -414333.312510] SLOW spr round 10 (radius: 5) [02:48:16 -414333.311230] SLOW spr round 11 (radius: 10) [02:50:35 -414333.310776] SLOW spr round 12 (radius: 15) [02:54:34 -414333.310520] SLOW spr round 13 (radius: 20) [03:00:13 -414333.310321] SLOW spr round 14 (radius: 25) [03:08:02 -414333.310139] Model parameter optimization (eps = 0.100000) [03:08:07] ML tree search #3, logLikelihood: -414333.214812 [03:08:07 -1365599.050569] Initial branch length optimization [03:08:11 -1150262.466670] Model parameter optimization (eps = 10.000000) [03:08:38 -1149038.058590] AUTODETECT spr round 1 (radius: 5) [03:10:27 -833828.433282] AUTODETECT spr round 2 (radius: 10) [03:12:47 -597621.861924] AUTODETECT spr round 3 (radius: 15) [03:15:04 -487997.610791] AUTODETECT spr round 4 (radius: 20) [03:17:39 -468333.623652] AUTODETECT spr round 5 (radius: 25) [03:20:55 -464717.278163] SPR radius for FAST iterations: 25 (autodetect) [03:20:55 -464717.278163] Model parameter optimization (eps = 3.000000) [03:21:29 -463922.291970] FAST spr round 1 (radius: 25) [03:24:26 -416201.979829] FAST spr round 2 (radius: 25) [03:26:31 -414548.083093] FAST spr round 3 (radius: 25) [03:28:24 -414483.317943] FAST spr round 4 (radius: 25) [03:29:58 -414482.706177] FAST spr round 5 (radius: 25) [03:31:27 -414482.705592] Model parameter optimization (eps = 1.000000) [03:31:38 -414474.901185] SLOW spr round 1 (radius: 5) [03:33:39 -414396.464387] SLOW spr round 2 (radius: 5) [03:35:34 -414389.757810] SLOW spr round 3 (radius: 5) [03:37:29 -414383.884393] SLOW spr round 4 (radius: 5) [03:39:21 -414383.643730] SLOW spr round 5 (radius: 5) [03:41:15 -414380.556429] SLOW spr round 6 (radius: 5) [03:43:05 -414380.550584] SLOW spr round 7 (radius: 10) [03:45:03 -414376.911639] SLOW spr round 8 (radius: 5) [03:47:25 -414361.762474] SLOW spr round 9 (radius: 5) [03:49:28 -414352.203464] SLOW spr round 10 (radius: 5) [03:51:23 -414351.218005] SLOW spr round 11 (radius: 5) [03:53:15 -414351.217953] SLOW spr round 12 (radius: 10) [03:55:15 -414343.618245] SLOW spr round 13 (radius: 5) [03:57:29 -414339.797907] SLOW spr round 14 (radius: 5) [03:59:29 -414339.795986] SLOW spr round 15 (radius: 10) [04:01:35 -414338.925853] SLOW spr round 16 (radius: 5) [04:03:48 -414338.542604] SLOW spr round 17 (radius: 5) [04:05:47 -414338.540278] SLOW spr round 18 (radius: 10) [04:07:52 -414338.540194] SLOW spr round 19 (radius: 15) [04:11:20 -414338.540192] SLOW spr round 20 (radius: 20) [04:16:14 -414338.540191] SLOW spr round 21 (radius: 25) [04:22:31 -414338.540191] Model parameter optimization (eps = 0.100000) [04:22:39] ML tree search #4, logLikelihood: -414338.171224 [04:22:39 -1378688.899456] Initial branch length optimization [04:22:44 -1164887.463656] Model parameter optimization (eps = 10.000000) [04:23:08 -1163564.576754] AUTODETECT spr round 1 (radius: 5) [04:24:56 -816977.412981] AUTODETECT spr round 2 (radius: 10) [04:27:03 -619261.646401] AUTODETECT spr round 3 (radius: 15) [04:29:09 -527075.962362] AUTODETECT spr round 4 (radius: 20) [04:31:26 -489282.168594] AUTODETECT spr round 5 (radius: 25) [04:34:09 -469177.901467] SPR radius for FAST iterations: 25 (autodetect) [04:34:09 -469177.901467] Model parameter optimization (eps = 3.000000) [04:34:38 -468631.860940] FAST spr round 1 (radius: 25) [04:37:19 -418094.319404] FAST spr round 2 (radius: 25) [04:39:27 -414656.452956] FAST spr round 3 (radius: 25) [04:41:15 -414479.461970] FAST spr round 4 (radius: 25) [04:42:50 -414469.302108] FAST spr round 5 (radius: 25) [04:44:21 -414462.489630] FAST spr round 6 (radius: 25) [04:45:48 -414462.476599] Model parameter optimization (eps = 1.000000) [04:46:04 -414438.933144] SLOW spr round 1 (radius: 5) [04:48:01 -414341.242889] SLOW spr round 2 (radius: 5) [04:49:58 -414329.190269] SLOW spr round 3 (radius: 5) [04:51:48 -414327.857570] SLOW spr round 4 (radius: 5) [04:53:39 -414326.449240] SLOW spr round 5 (radius: 5) [04:55:30 -414326.446932] SLOW spr round 6 (radius: 10) [04:57:31 -414319.591977] SLOW spr round 7 (radius: 5) [04:59:45 -414318.909277] SLOW spr round 8 (radius: 5) [05:01:46 -414318.902179] SLOW spr round 9 (radius: 10) [05:03:53 -414317.198041] SLOW spr round 10 (radius: 5) [05:06:06 -414317.185327] SLOW spr round 11 (radius: 10) [05:08:22 -414316.584067] SLOW spr round 12 (radius: 5) [05:10:33 -414316.578931] SLOW spr round 13 (radius: 10) [05:12:47 -414316.578112] SLOW spr round 14 (radius: 15) [05:16:08 -414314.384741] SLOW spr round 15 (radius: 5) [05:18:28 -414313.637864] SLOW spr round 16 (radius: 5) [05:20:32 -414313.637848] SLOW spr round 17 (radius: 10) [05:22:40 -414313.637842] SLOW spr round 18 (radius: 15) [05:26:05 -414313.637839] SLOW spr round 19 (radius: 20) [05:31:01 -414313.637838] SLOW spr round 20 (radius: 25) [05:37:22 -414313.637837] Model parameter optimization (eps = 0.100000) [05:37:32] ML tree search #5, logLikelihood: -414313.034908 [05:37:32 -1371673.078882] Initial branch length optimization [05:37:36 -1157636.193810] Model parameter optimization (eps = 10.000000) [05:38:01 -1156240.073972] AUTODETECT spr round 1 (radius: 5) [05:39:50 -815084.541030] AUTODETECT spr round 2 (radius: 10) [05:41:59 -628632.028945] AUTODETECT spr round 3 (radius: 15) [05:44:03 -552680.504166] AUTODETECT spr round 4 (radius: 20) [05:46:27 -495689.227957] AUTODETECT spr round 5 (radius: 25) [05:49:28 -476683.025527] SPR radius for FAST iterations: 25 (autodetect) [05:49:28 -476683.025527] Model parameter optimization (eps = 3.000000) [05:49:55 -476164.166344] FAST spr round 1 (radius: 25) [05:52:37 -417055.533641] FAST spr round 2 (radius: 25) [05:54:48 -414591.139285] FAST spr round 3 (radius: 25) [05:56:35 -414520.365044] FAST spr round 4 (radius: 25) [05:58:11 -414509.533405] FAST spr round 5 (radius: 25) [05:59:42 -414507.035086] FAST spr round 6 (radius: 25) [06:01:10 -414507.033967] Model parameter optimization (eps = 1.000000) [06:01:26 -414434.789959] SLOW spr round 1 (radius: 5) [06:03:27 -414355.972334] SLOW spr round 2 (radius: 5) [06:05:24 -414351.838359] SLOW spr round 3 (radius: 5) [06:07:16 -414351.837154] SLOW spr round 4 (radius: 10) [06:09:21 -414343.383619] SLOW spr round 5 (radius: 5) [06:11:38 -414341.021032] SLOW spr round 6 (radius: 5) [06:13:41 -414338.377785] SLOW spr round 7 (radius: 5) [06:15:38 -414338.376699] SLOW spr round 8 (radius: 10) [06:17:44 -414332.351953] SLOW spr round 9 (radius: 5) [06:20:00 -414330.584069] SLOW spr round 10 (radius: 5) [06:22:02 -414330.583466] SLOW spr round 11 (radius: 10) [06:24:11 -414329.882765] SLOW spr round 12 (radius: 5) [06:26:25 -414329.882030] SLOW spr round 13 (radius: 10) [06:28:45 -414329.881889] SLOW spr round 14 (radius: 15) [06:32:14 -414329.745697] SLOW spr round 15 (radius: 5) [06:34:37 -414328.875172] SLOW spr round 16 (radius: 5) [06:36:43 -414328.873491] SLOW spr round 17 (radius: 10) [06:38:55 -414328.873013] SLOW spr round 18 (radius: 15) [06:42:31 -414328.872872] SLOW spr round 19 (radius: 20) [06:47:41 -414328.872829] SLOW spr round 20 (radius: 25) [06:54:41 -414328.872816] Model parameter optimization (eps = 0.100000) [06:54:47] ML tree search #6, logLikelihood: -414328.742469 [06:54:48 -1369831.709149] Initial branch length optimization [06:54:51 -1157471.110762] Model parameter optimization (eps = 10.000000) [06:55:35 -1155688.169993] AUTODETECT spr round 1 (radius: 5) [06:57:23 -820143.187878] AUTODETECT spr round 2 (radius: 10) [06:59:31 -592188.696055] AUTODETECT spr round 3 (radius: 15) [07:01:33 -489076.831892] AUTODETECT spr round 4 (radius: 20) [07:03:45 -471448.770090] AUTODETECT spr round 5 (radius: 25) [07:06:20 -461907.605173] SPR radius for FAST iterations: 25 (autodetect) [07:06:20 -461907.605173] Model parameter optimization (eps = 3.000000) [07:06:42 -461149.769062] FAST spr round 1 (radius: 25) [07:09:17 -417346.615685] FAST spr round 2 (radius: 25) [07:11:22 -414670.019780] FAST spr round 3 (radius: 25) [07:13:10 -414495.570894] FAST spr round 4 (radius: 25) [07:14:45 -414483.945999] FAST spr round 5 (radius: 25) [07:16:15 -414473.574690] FAST spr round 6 (radius: 25) [07:17:42 -414473.573606] Model parameter optimization (eps = 1.000000) [07:17:59 -414431.148923] SLOW spr round 1 (radius: 5) [07:19:55 -414353.683647] SLOW spr round 2 (radius: 5) [07:21:50 -414345.598081] SLOW spr round 3 (radius: 5) [07:23:41 -414345.595829] SLOW spr round 4 (radius: 10) [07:25:41 -414339.536342] SLOW spr round 5 (radius: 5) [07:27:58 -414326.091062] SLOW spr round 6 (radius: 5) [07:30:00 -414326.087900] SLOW spr round 7 (radius: 10) [07:32:05 -414326.087827] SLOW spr round 8 (radius: 15) [07:35:36 -414326.087825] SLOW spr round 9 (radius: 20) [07:40:34 -414326.087825] SLOW spr round 10 (radius: 25) [07:47:06 -414326.087825] Model parameter optimization (eps = 0.100000) [07:47:13] ML tree search #7, logLikelihood: -414325.530694 [07:47:13 -1372617.488483] Initial branch length optimization [07:47:17 -1152784.684024] Model parameter optimization (eps = 10.000000) [07:47:45 -1151267.674600] AUTODETECT spr round 1 (radius: 5) [07:49:33 -833144.647044] AUTODETECT spr round 2 (radius: 10) [07:51:41 -625818.085310] AUTODETECT spr round 3 (radius: 15) [07:53:40 -526639.772814] AUTODETECT spr round 4 (radius: 20) [07:55:58 -481864.617759] AUTODETECT spr round 5 (radius: 25) [07:58:32 -467757.328957] SPR radius for FAST iterations: 25 (autodetect) [07:58:32 -467757.328957] Model parameter optimization (eps = 3.000000) [07:58:59 -467124.046170] FAST spr round 1 (radius: 25) [08:01:37 -416753.324957] FAST spr round 2 (radius: 25) [08:03:43 -414563.165690] FAST spr round 3 (radius: 25) [08:05:33 -414429.890075] FAST spr round 4 (radius: 25) [08:07:07 -414409.401017] FAST spr round 5 (radius: 25) [08:08:36 -414409.398434] Model parameter optimization (eps = 1.000000) [08:08:51 -414378.945014] SLOW spr round 1 (radius: 5) [08:10:52 -414320.927250] SLOW spr round 2 (radius: 5) [08:12:47 -414315.658498] SLOW spr round 3 (radius: 5) [08:14:39 -414315.378647] SLOW spr round 4 (radius: 5) [08:16:29 -414315.377300] SLOW spr round 5 (radius: 10) [08:18:29 -414314.438371] SLOW spr round 6 (radius: 5) [08:20:43 -414314.437880] SLOW spr round 7 (radius: 10) [08:23:02 -414314.437615] SLOW spr round 8 (radius: 15) [08:26:27 -414314.437396] SLOW spr round 9 (radius: 20) [08:31:30 -414314.437198] SLOW spr round 10 (radius: 25) [08:38:00 -414314.437011] Model parameter optimization (eps = 0.100000) [08:38:15] ML tree search #8, logLikelihood: -414313.868626 [08:38:15 -1366593.536016] Initial branch length optimization [08:38:19 -1148603.511377] Model parameter optimization (eps = 10.000000) [08:38:48 -1147158.075330] AUTODETECT spr round 1 (radius: 5) [08:40:49 -820896.321787] AUTODETECT spr round 2 (radius: 10) [08:43:19 -620920.530225] AUTODETECT spr round 3 (radius: 15) [08:45:37 -497587.297464] AUTODETECT spr round 4 (radius: 20) [08:47:57 -463822.260842] AUTODETECT spr round 5 (radius: 25) [08:50:45 -462879.081166] SPR radius for FAST iterations: 25 (autodetect) [08:50:45 -462879.081166] Model parameter optimization (eps = 3.000000) [08:51:14 -462232.836730] FAST spr round 1 (radius: 25) [08:53:52 -416665.881492] FAST spr round 2 (radius: 25) [08:56:03 -414686.234339] FAST spr round 3 (radius: 25) [08:57:56 -414486.256492] FAST spr round 4 (radius: 25) [08:59:38 -414448.700057] FAST spr round 5 (radius: 25) [09:01:13 -414437.427916] FAST spr round 6 (radius: 25) [09:02:44 -414429.893329] FAST spr round 7 (radius: 25) [09:04:11 -414429.892536] Model parameter optimization (eps = 1.000000) [09:04:21 -414420.430320] SLOW spr round 1 (radius: 5) [09:06:22 -414361.917146] SLOW spr round 2 (radius: 5) [09:08:19 -414350.322986] SLOW spr round 3 (radius: 5) [09:10:10 -414350.321699] SLOW spr round 4 (radius: 10) [09:12:11 -414343.125349] SLOW spr round 5 (radius: 5) [09:14:31 -414324.139218] SLOW spr round 6 (radius: 5) [09:16:34 -414319.490680] SLOW spr round 7 (radius: 5) [09:18:30 -414319.246162] SLOW spr round 8 (radius: 5) [09:20:22 -414319.244665] SLOW spr round 9 (radius: 10) [09:22:22 -414318.504504] SLOW spr round 10 (radius: 5) [09:24:39 -414315.542867] SLOW spr round 11 (radius: 5) [09:26:40 -414315.541426] SLOW spr round 12 (radius: 10) [09:28:44 -414315.541369] SLOW spr round 13 (radius: 15) [09:32:14 -414315.541364] SLOW spr round 14 (radius: 20) [09:37:10 -414315.541363] SLOW spr round 15 (radius: 25) [09:43:43 -414315.541362] Model parameter optimization (eps = 0.100000) [09:43:52] ML tree search #9, logLikelihood: -414315.082085 [09:43:52 -1367820.987495] Initial branch length optimization [09:43:58 -1150528.856154] Model parameter optimization (eps = 10.000000) [09:44:28 -1149073.736275] AUTODETECT spr round 1 (radius: 5) [09:46:15 -818801.353991] AUTODETECT spr round 2 (radius: 10) [09:48:30 -637060.656748] AUTODETECT spr round 3 (radius: 15) [09:50:36 -546637.984630] AUTODETECT spr round 4 (radius: 20) [09:53:03 -475489.637109] AUTODETECT spr round 5 (radius: 25) [09:55:46 -469464.025038] SPR radius for FAST iterations: 25 (autodetect) [09:55:46 -469464.025038] Model parameter optimization (eps = 3.000000) [09:56:03 -468872.080637] FAST spr round 1 (radius: 25) [09:58:48 -416651.950795] FAST spr round 2 (radius: 25) [10:00:54 -414699.626216] FAST spr round 3 (radius: 25) [10:02:43 -414533.057415] FAST spr round 4 (radius: 25) [10:04:17 -414519.546511] FAST spr round 5 (radius: 25) [10:05:48 -414491.874758] FAST spr round 6 (radius: 25) [10:07:16 -414483.972590] FAST spr round 7 (radius: 25) [10:08:43 -414483.971783] Model parameter optimization (eps = 1.000000) [10:08:56 -414444.305160] SLOW spr round 1 (radius: 5) [10:10:56 -414366.390938] SLOW spr round 2 (radius: 5) [10:12:51 -414359.248858] SLOW spr round 3 (radius: 5) [10:14:42 -414359.247276] SLOW spr round 4 (radius: 10) [10:16:42 -414358.853219] SLOW spr round 5 (radius: 5) [10:18:58 -414358.166632] SLOW spr round 6 (radius: 5) [10:21:00 -414358.165204] SLOW spr round 7 (radius: 10) [10:23:06 -414357.772478] SLOW spr round 8 (radius: 5) [10:25:23 -414340.486006] SLOW spr round 9 (radius: 5) [10:27:25 -414338.324035] SLOW spr round 10 (radius: 5) [10:29:20 -414338.323836] SLOW spr round 11 (radius: 10) [10:31:21 -414338.217072] SLOW spr round 12 (radius: 5) [10:33:35 -414338.212578] SLOW spr round 13 (radius: 10) [10:35:52 -414338.212210] SLOW spr round 14 (radius: 15) [10:39:12 -414338.212164] SLOW spr round 15 (radius: 20) [10:44:13 -414338.212154] SLOW spr round 16 (radius: 25) [10:50:48 -414338.212151] Model parameter optimization (eps = 0.100000) [10:50:58] ML tree search #10, logLikelihood: -414338.075033 [10:50:58 -1368380.684543] Initial branch length optimization [10:51:02 -1154187.760940] Model parameter optimization (eps = 10.000000) [10:51:23 -1152842.182927] AUTODETECT spr round 1 (radius: 5) [10:53:12 -819954.648572] AUTODETECT spr round 2 (radius: 10) [10:55:24 -598583.894016] AUTODETECT spr round 3 (radius: 15) [10:57:25 -518194.315263] AUTODETECT spr round 4 (radius: 20) [10:59:47 -468731.082942] AUTODETECT spr round 5 (radius: 25) [11:02:37 -463022.272622] SPR radius for FAST iterations: 25 (autodetect) [11:02:37 -463022.272622] Model parameter optimization (eps = 3.000000) [11:02:54 -462375.193550] FAST spr round 1 (radius: 25) [11:05:42 -416536.703937] FAST spr round 2 (radius: 25) [11:07:47 -414602.401231] FAST spr round 3 (radius: 25) [11:09:38 -414513.251741] FAST spr round 4 (radius: 25) [11:11:15 -414503.918871] FAST spr round 5 (radius: 25) [11:12:44 -414503.917214] Model parameter optimization (eps = 1.000000) [11:13:03 -414454.173373] SLOW spr round 1 (radius: 5) [11:15:01 -414379.290567] SLOW spr round 2 (radius: 5) [11:16:57 -414370.429557] SLOW spr round 3 (radius: 5) [11:18:49 -414370.422123] SLOW spr round 4 (radius: 10) [11:20:51 -414359.195079] SLOW spr round 5 (radius: 5) [11:23:09 -414340.994474] SLOW spr round 6 (radius: 5) [11:25:11 -414340.769165] SLOW spr round 7 (radius: 5) [11:27:07 -414340.765131] SLOW spr round 8 (radius: 10) [11:29:10 -414337.458800] SLOW spr round 9 (radius: 5) [11:31:28 -414316.691932] SLOW spr round 10 (radius: 5) [11:33:29 -414315.467257] SLOW spr round 11 (radius: 5) [11:35:24 -414315.465535] SLOW spr round 12 (radius: 10) [11:37:25 -414315.181932] SLOW spr round 13 (radius: 5) [11:39:38 -414315.172371] SLOW spr round 14 (radius: 10) [11:41:55 -414314.740175] SLOW spr round 15 (radius: 5) [11:44:07 -414309.024583] SLOW spr round 16 (radius: 5) [11:46:08 -414306.404067] SLOW spr round 17 (radius: 5) [11:48:03 -414301.748248] SLOW spr round 18 (radius: 5) [11:49:55 -414301.746803] SLOW spr round 19 (radius: 10) [11:51:54 -414301.746687] SLOW spr round 20 (radius: 15) [11:55:31 -414301.746679] SLOW spr round 21 (radius: 20) [12:00:32 -414301.746678] SLOW spr round 22 (radius: 25) [12:07:16 -414301.746678] Model parameter optimization (eps = 0.100000) [12:07:24] ML tree search #11, logLikelihood: -414301.333653 [12:07:24 -1372589.709562] Initial branch length optimization [12:07:29 -1157316.055327] Model parameter optimization (eps = 10.000000) [12:07:59 -1155933.092650] AUTODETECT spr round 1 (radius: 5) [12:09:48 -820759.041666] AUTODETECT spr round 2 (radius: 10) [12:11:59 -628880.982515] AUTODETECT spr round 3 (radius: 15) [12:14:03 -516723.490098] AUTODETECT spr round 4 (radius: 20) [12:16:29 -471985.412069] AUTODETECT spr round 5 (radius: 25) [12:19:25 -464875.329714] SPR radius for FAST iterations: 25 (autodetect) [12:19:25 -464875.329714] Model parameter optimization (eps = 3.000000) [12:19:49 -464217.506974] FAST spr round 1 (radius: 25) [12:22:25 -416721.480305] FAST spr round 2 (radius: 25) [12:24:34 -414864.092875] FAST spr round 3 (radius: 25) [12:26:28 -414523.436999] FAST spr round 4 (radius: 25) [12:28:05 -414483.990502] FAST spr round 5 (radius: 25) [12:29:37 -414455.601101] FAST spr round 6 (radius: 25) [12:31:04 -414455.600118] Model parameter optimization (eps = 1.000000) [12:31:18 -414410.858057] SLOW spr round 1 (radius: 5) [12:33:17 -414328.340358] SLOW spr round 2 (radius: 5) [12:35:11 -414321.439038] SLOW spr round 3 (radius: 5) [12:37:05 -414316.780794] SLOW spr round 4 (radius: 5) [12:38:57 -414316.779323] SLOW spr round 5 (radius: 10) [12:40:58 -414311.488604] SLOW spr round 6 (radius: 5) [12:43:18 -414297.941062] SLOW spr round 7 (radius: 5) [12:45:20 -414297.936537] SLOW spr round 8 (radius: 10) [12:47:25 -414297.936271] SLOW spr round 9 (radius: 15) [12:50:56 -414297.936074] SLOW spr round 10 (radius: 20) [12:55:53 -414297.935879] SLOW spr round 11 (radius: 25) [13:02:26 -414297.935684] Model parameter optimization (eps = 0.100000) [13:02:33] ML tree search #12, logLikelihood: -414297.732006 [13:02:33 -1370476.695132] Initial branch length optimization [13:02:37 -1154721.935059] Model parameter optimization (eps = 10.000000) [13:03:05 -1153476.037641] AUTODETECT spr round 1 (radius: 5) [13:04:54 -823684.438159] AUTODETECT spr round 2 (radius: 10) [13:07:05 -621024.838554] AUTODETECT spr round 3 (radius: 15) [13:09:07 -556933.188432] AUTODETECT spr round 4 (radius: 20) [13:11:35 -488526.998948] AUTODETECT spr round 5 (radius: 25) [13:14:16 -475723.583547] SPR radius for FAST iterations: 25 (autodetect) [13:14:17 -475723.583547] Model parameter optimization (eps = 3.000000) [13:14:45 -475230.935124] FAST spr round 1 (radius: 25) [13:17:25 -417789.822319] FAST spr round 2 (radius: 25) [13:19:28 -414668.233204] FAST spr round 3 (radius: 25) [13:21:19 -414516.295324] FAST spr round 4 (radius: 25) [13:23:00 -414471.803913] FAST spr round 5 (radius: 25) [13:24:31 -414452.577137] FAST spr round 6 (radius: 25) [13:26:00 -414449.947246] FAST spr round 7 (radius: 25) [13:27:26 -414449.945369] Model parameter optimization (eps = 1.000000) [13:27:41 -414424.522485] SLOW spr round 1 (radius: 5) [13:29:40 -414350.912618] SLOW spr round 2 (radius: 5) [13:31:34 -414345.073943] SLOW spr round 3 (radius: 5) [13:33:28 -414341.927911] SLOW spr round 4 (radius: 5) [13:35:20 -414341.592398] SLOW spr round 5 (radius: 5) [13:37:10 -414341.592150] SLOW spr round 6 (radius: 10) [13:39:11 -414336.311015] SLOW spr round 7 (radius: 5) [13:41:30 -414321.999110] SLOW spr round 8 (radius: 5) [13:43:31 -414321.992725] SLOW spr round 9 (radius: 10) [13:45:37 -414321.312630] SLOW spr round 10 (radius: 5) [13:47:51 -414321.309585] SLOW spr round 11 (radius: 10) [13:50:07 -414321.309341] SLOW spr round 12 (radius: 15) [13:53:29 -414320.949072] SLOW spr round 13 (radius: 5) [13:55:49 -414320.234612] SLOW spr round 14 (radius: 5) [13:57:54 -414320.233123] SLOW spr round 15 (radius: 10) [14:00:02 -414320.232796] SLOW spr round 16 (radius: 15) [14:03:32 -414320.232576] SLOW spr round 17 (radius: 20) [14:08:37 -414320.232367] SLOW spr round 18 (radius: 25) [14:15:12 -414320.232171] Model parameter optimization (eps = 0.100000) [14:15:20] ML tree search #13, logLikelihood: -414319.835584 [14:15:20 -1367763.184441] Initial branch length optimization [14:15:26 -1157932.738996] Model parameter optimization (eps = 10.000000) [14:15:50 -1156538.445538] AUTODETECT spr round 1 (radius: 5) [14:17:38 -820059.366987] AUTODETECT spr round 2 (radius: 10) [14:19:50 -603549.282969] AUTODETECT spr round 3 (radius: 15) [14:21:58 -505505.687222] AUTODETECT spr round 4 (radius: 20) [14:24:28 -466607.946838] AUTODETECT spr round 5 (radius: 25) [14:27:22 -463885.913904] SPR radius for FAST iterations: 25 (autodetect) [14:27:22 -463885.913904] Model parameter optimization (eps = 3.000000) [14:27:44 -463303.158307] FAST spr round 1 (radius: 25) [14:30:20 -416990.905955] FAST spr round 2 (radius: 25) [14:32:24 -414741.114766] FAST spr round 3 (radius: 25) [14:34:14 -414549.073450] FAST spr round 4 (radius: 25) [14:35:49 -414526.422442] FAST spr round 5 (radius: 25) [14:37:18 -414526.410257] Model parameter optimization (eps = 1.000000) [14:37:37 -414463.328222] SLOW spr round 1 (radius: 5) [14:39:36 -414391.829936] SLOW spr round 2 (radius: 5) [14:41:30 -414387.611450] SLOW spr round 3 (radius: 5) [14:43:22 -414387.569461] SLOW spr round 4 (radius: 10) [14:45:25 -414378.640404] SLOW spr round 5 (radius: 5) [14:47:44 -414363.816837] SLOW spr round 6 (radius: 5) [14:49:45 -414363.801543] SLOW spr round 7 (radius: 10) [14:51:50 -414363.801204] SLOW spr round 8 (radius: 15) [14:55:21 -414345.235719] SLOW spr round 9 (radius: 5) [14:57:41 -414340.639401] SLOW spr round 10 (radius: 5) [14:59:44 -414340.523530] SLOW spr round 11 (radius: 5) [15:01:40 -414340.522812] SLOW spr round 12 (radius: 10) [15:03:42 -414340.522771] SLOW spr round 13 (radius: 15) [15:07:12 -414340.522765] SLOW spr round 14 (radius: 20) [15:12:02 -414340.522764] SLOW spr round 15 (radius: 25) [15:18:21 -414340.522763] Model parameter optimization (eps = 0.100000) [15:18:29] ML tree search #14, logLikelihood: -414340.039368 [15:18:29 -1367107.182424] Initial branch length optimization [15:18:35 -1150460.291859] Model parameter optimization (eps = 10.000000) [15:19:24 -1149100.998437] AUTODETECT spr round 1 (radius: 5) [15:21:11 -799557.839618] AUTODETECT spr round 2 (radius: 10) [15:23:18 -587641.356345] AUTODETECT spr round 3 (radius: 15) [15:25:22 -517023.796888] AUTODETECT spr round 4 (radius: 20) [15:27:55 -475179.712136] AUTODETECT spr round 5 (radius: 25) [15:31:04 -464622.532724] SPR radius for FAST iterations: 25 (autodetect) [15:31:04 -464622.532724] Model parameter optimization (eps = 3.000000) [15:31:09 -464614.937557] FAST spr round 1 (radius: 25) [15:33:44 -417987.230447] FAST spr round 2 (radius: 25) [15:35:50 -415576.122821] FAST spr round 3 (radius: 25) [15:37:37 -415273.467271] FAST spr round 4 (radius: 25) [15:39:14 -415243.843387] FAST spr round 5 (radius: 25) [15:40:43 -415243.815815] Model parameter optimization (eps = 1.000000) [15:41:09 -414481.521089] SLOW spr round 1 (radius: 5) [15:43:10 -414372.335507] SLOW spr round 2 (radius: 5) [15:45:06 -414363.469299] SLOW spr round 3 (radius: 5) [15:46:58 -414362.442708] SLOW spr round 4 (radius: 5) [15:48:49 -414362.438198] SLOW spr round 5 (radius: 10) [15:50:53 -414348.477539] SLOW spr round 6 (radius: 5) [15:53:12 -414320.051264] SLOW spr round 7 (radius: 5) [15:55:14 -414320.048959] SLOW spr round 8 (radius: 10) [15:57:20 -414320.048460] SLOW spr round 9 (radius: 15) [16:00:55 -414320.048129] SLOW spr round 10 (radius: 20) [16:06:14 -414320.047815] SLOW spr round 11 (radius: 25) [16:13:22 -414320.047506] Model parameter optimization (eps = 0.100000) [16:13:30] ML tree search #15, logLikelihood: -414319.673438 [16:13:30 -1368873.584179] Initial branch length optimization [16:13:35 -1149872.952420] Model parameter optimization (eps = 10.000000) [16:14:15 -1148558.675539] AUTODETECT spr round 1 (radius: 5) [16:16:04 -805132.293107] AUTODETECT spr round 2 (radius: 10) [16:18:14 -611225.372419] AUTODETECT spr round 3 (radius: 15) [16:20:23 -503566.399923] AUTODETECT spr round 4 (radius: 20) [16:22:36 -467533.783616] AUTODETECT spr round 5 (radius: 25) [16:25:22 -460435.815167] SPR radius for FAST iterations: 25 (autodetect) [16:25:22 -460435.815167] Model parameter optimization (eps = 3.000000) [16:25:41 -459796.397174] FAST spr round 1 (radius: 25) [16:28:15 -415970.597676] FAST spr round 2 (radius: 25) [16:30:19 -414574.334490] FAST spr round 3 (radius: 25) [16:32:12 -414476.031188] FAST spr round 4 (radius: 25) [16:33:48 -414458.380673] FAST spr round 5 (radius: 25) [16:35:18 -414453.912796] FAST spr round 6 (radius: 25) [16:36:46 -414453.912085] Model parameter optimization (eps = 1.000000) [16:37:00 -414427.097565] SLOW spr round 1 (radius: 5) [16:38:59 -414359.276846] SLOW spr round 2 (radius: 5) [16:40:56 -414352.539468] SLOW spr round 3 (radius: 5) [16:42:50 -414348.414936] SLOW spr round 4 (radius: 5) [16:44:42 -414348.401506] SLOW spr round 5 (radius: 10) [16:46:44 -414345.681057] SLOW spr round 6 (radius: 5) [16:49:02 -414330.841311] SLOW spr round 7 (radius: 5) [16:51:04 -414330.798133] SLOW spr round 8 (radius: 10) [16:53:10 -414327.935151] SLOW spr round 9 (radius: 5) [16:55:30 -414327.931100] SLOW spr round 10 (radius: 10) [16:57:59 -414327.930661] SLOW spr round 11 (radius: 15) [17:01:39 -414327.381582] SLOW spr round 12 (radius: 5) [17:04:14 -414325.270400] SLOW spr round 13 (radius: 5) [17:06:30 -414325.270218] SLOW spr round 14 (radius: 10) [17:08:48 -414325.270134] SLOW spr round 15 (radius: 15) [17:12:37 -414325.270092] SLOW spr round 16 (radius: 20) [17:18:03 -414325.270072] SLOW spr round 17 (radius: 25) [17:25:13 -414325.270062] Model parameter optimization (eps = 0.100000) [17:25:24] ML tree search #16, logLikelihood: -414324.789066 [17:25:24 -1368129.719962] Initial branch length optimization [17:25:30 -1155712.844177] Model parameter optimization (eps = 10.000000) [17:26:01 -1154407.445977] AUTODETECT spr round 1 (radius: 5) [17:28:00 -824338.032499] AUTODETECT spr round 2 (radius: 10) [17:30:21 -631660.996110] AUTODETECT spr round 3 (radius: 15) [17:32:37 -557458.619861] AUTODETECT spr round 4 (radius: 20) [17:35:20 -496373.257758] AUTODETECT spr round 5 (radius: 25) [17:38:27 -474546.513301] SPR radius for FAST iterations: 25 (autodetect) [17:38:27 -474546.513301] Model parameter optimization (eps = 3.000000) [17:39:01 -473936.141358] FAST spr round 1 (radius: 25) [17:41:53 -416631.821473] FAST spr round 2 (radius: 25) [17:44:06 -414688.084972] FAST spr round 3 (radius: 25) [17:46:02 -414548.889441] FAST spr round 4 (radius: 25) [17:47:47 -414505.890113] FAST spr round 5 (radius: 25) [17:49:25 -414500.171371] FAST spr round 6 (radius: 25) [17:50:59 -414500.170105] Model parameter optimization (eps = 1.000000) [17:51:21 -414459.827578] SLOW spr round 1 (radius: 5) [17:53:27 -414351.732228] SLOW spr round 2 (radius: 5) [17:55:33 -414346.247555] SLOW spr round 3 (radius: 5) [17:57:36 -414345.817874] SLOW spr round 4 (radius: 5) [17:59:37 -414345.809886] SLOW spr round 5 (radius: 10) [18:01:47 -414344.265303] SLOW spr round 6 (radius: 5) [18:04:16 -414328.439816] SLOW spr round 7 (radius: 5) [18:06:29 -414328.439372] SLOW spr round 8 (radius: 10) [18:08:44 -414327.231789] SLOW spr round 9 (radius: 5) [18:11:10 -414326.525863] SLOW spr round 10 (radius: 5) [18:13:21 -414326.524880] SLOW spr round 11 (radius: 10) [18:15:36 -414326.524827] SLOW spr round 12 (radius: 15) [18:19:20 -414326.524810] SLOW spr round 13 (radius: 20) [18:24:38 -414326.524800] SLOW spr round 14 (radius: 25) [18:31:41 -414326.524794] Model parameter optimization (eps = 0.100000) [18:31:46] ML tree search #17, logLikelihood: -414326.494555 [18:31:46 -1374692.752561] Initial branch length optimization [18:31:51 -1154214.185072] Model parameter optimization (eps = 10.000000) [18:32:21 -1153051.624297] AUTODETECT spr round 1 (radius: 5) [18:34:19 -815388.243875] AUTODETECT spr round 2 (radius: 10) [18:36:44 -624370.333277] AUTODETECT spr round 3 (radius: 15) [18:39:00 -557453.123369] AUTODETECT spr round 4 (radius: 20) [18:41:42 -488605.376897] AUTODETECT spr round 5 (radius: 25) [18:45:08 -477948.790061] SPR radius for FAST iterations: 25 (autodetect) [18:45:08 -477948.790061] Model parameter optimization (eps = 3.000000) [18:45:26 -477480.731494] FAST spr round 1 (radius: 25) [18:48:27 -417030.685051] FAST spr round 2 (radius: 25) [18:50:44 -414712.206372] FAST spr round 3 (radius: 25) [18:52:44 -414574.279960] FAST spr round 4 (radius: 25) [18:54:29 -414551.907750] FAST spr round 5 (radius: 25) [18:56:08 -414539.926724] FAST spr round 6 (radius: 25) [18:57:43 -414539.924515] Model parameter optimization (eps = 1.000000) [18:58:11 -414422.239237] SLOW spr round 1 (radius: 5) [19:00:18 -414351.582017] SLOW spr round 2 (radius: 5) [19:02:25 -414341.749534] SLOW spr round 3 (radius: 5) [19:04:27 -414341.671851] SLOW spr round 4 (radius: 10) [19:06:37 -414335.843598] SLOW spr round 5 (radius: 5) [19:09:05 -414332.803251] SLOW spr round 6 (radius: 5) [19:11:18 -414332.790573] SLOW spr round 7 (radius: 10) [19:13:33 -414332.790212] SLOW spr round 8 (radius: 15) [19:17:24 -414332.790016] SLOW spr round 9 (radius: 20) [19:23:02 -414332.789841] SLOW spr round 10 (radius: 25) [19:30:42 -414332.789669] Model parameter optimization (eps = 0.100000) [19:30:47] ML tree search #18, logLikelihood: -414332.767103 [19:30:47 -1366119.234176] Initial branch length optimization [19:30:53 -1150312.099387] Model parameter optimization (eps = 10.000000) [19:31:21 -1148914.692730] AUTODETECT spr round 1 (radius: 5) [19:33:19 -826329.014827] AUTODETECT spr round 2 (radius: 10) [19:35:40 -615784.482539] AUTODETECT spr round 3 (radius: 15) [19:37:59 -514683.353853] AUTODETECT spr round 4 (radius: 20) [19:40:29 -482525.053521] AUTODETECT spr round 5 (radius: 25) [19:43:39 -470020.337333] SPR radius for FAST iterations: 25 (autodetect) [19:43:39 -470020.337333] Model parameter optimization (eps = 3.000000) [19:44:07 -469288.165951] FAST spr round 1 (radius: 25) [19:47:00 -416454.734975] FAST spr round 2 (radius: 25) [19:49:20 -414624.066193] FAST spr round 3 (radius: 25) [19:51:23 -414499.691095] FAST spr round 4 (radius: 25) [19:53:11 -414467.504292] FAST spr round 5 (radius: 25) [19:54:52 -414460.266821] FAST spr round 6 (radius: 25) [19:56:28 -414458.835164] FAST spr round 7 (radius: 25) [19:58:01 -414458.835160] Model parameter optimization (eps = 1.000000) [19:58:20 -414426.949925] SLOW spr round 1 (radius: 5) [20:00:31 -414358.898516] SLOW spr round 2 (radius: 5) [20:02:39 -414354.185416] SLOW spr round 3 (radius: 5) [20:04:40 -414353.969928] SLOW spr round 4 (radius: 5) [20:06:41 -414353.968297] SLOW spr round 5 (radius: 10) [20:08:54 -414347.539244] SLOW spr round 6 (radius: 5) [20:11:25 -414328.704810] SLOW spr round 7 (radius: 5) [20:13:38 -414327.415447] SLOW spr round 8 (radius: 5) [20:15:43 -414327.412124] SLOW spr round 9 (radius: 10) [20:17:56 -414327.411910] SLOW spr round 10 (radius: 15) [20:21:58 -414327.411719] SLOW spr round 11 (radius: 20) [20:27:33 -414327.411532] SLOW spr round 12 (radius: 25) [20:35:09 -414327.411347] Model parameter optimization (eps = 0.100000) [20:35:16] ML tree search #19, logLikelihood: -414327.361945 [20:35:16 -1371263.010840] Initial branch length optimization [20:35:22 -1156511.666337] Model parameter optimization (eps = 10.000000) [20:35:51 -1155272.951186] AUTODETECT spr round 1 (radius: 5) [20:37:51 -845574.617818] AUTODETECT spr round 2 (radius: 10) [20:40:17 -612260.523662] AUTODETECT spr round 3 (radius: 15) [20:42:34 -512392.383275] AUTODETECT spr round 4 (radius: 20) [20:45:25 -468123.463708] AUTODETECT spr round 5 (radius: 25) [20:49:01 -464183.952432] SPR radius for FAST iterations: 25 (autodetect) [20:49:01 -464183.952432] Model parameter optimization (eps = 3.000000) [20:49:09 -464175.364306] FAST spr round 1 (radius: 25) [20:52:10 -417464.062539] FAST spr round 2 (radius: 25) [20:54:33 -415417.494930] FAST spr round 3 (radius: 25) [20:56:34 -415310.847880] FAST spr round 4 (radius: 25) [20:58:24 -415265.468885] FAST spr round 5 (radius: 25) [21:00:06 -415255.712558] FAST spr round 6 (radius: 25) [21:01:42 -415255.710476] Model parameter optimization (eps = 1.000000) [21:02:09 -414481.910115] SLOW spr round 1 (radius: 5) [21:04:21 -414365.815688] SLOW spr round 2 (radius: 5) [21:06:26 -414360.861848] SLOW spr round 3 (radius: 5) [21:08:28 -414360.625316] SLOW spr round 4 (radius: 5) [21:10:30 -414360.618781] SLOW spr round 5 (radius: 10) [21:12:44 -414352.051148] SLOW spr round 6 (radius: 5) [21:15:16 -414345.186863] SLOW spr round 7 (radius: 5) [21:17:31 -414345.172490] SLOW spr round 8 (radius: 10) [21:19:52 -414342.554052] SLOW spr round 9 (radius: 5) [21:22:20 -414342.097404] SLOW spr round 10 (radius: 5) [21:24:35 -414341.509641] SLOW spr round 11 (radius: 5) [21:26:42 -414341.508574] SLOW spr round 12 (radius: 10) [21:28:57 -414341.508477] SLOW spr round 13 (radius: 15) [21:33:01 -414341.508461] SLOW spr round 14 (radius: 20) [21:38:30 -414341.508458] SLOW spr round 15 (radius: 25) [21:45:55 -414341.508456] Model parameter optimization (eps = 0.100000) [21:46:09] ML tree search #20, logLikelihood: -414338.781537 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.061299,0.585396) (0.208606,0.808894) (0.218413,0.583492) (0.511682,1.305368) 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: -414297.732006 AIC score: 832605.464013 / AICc score: 8876665.464013 / BIC score: 842232.036497 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=899). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A8TX70/3_mltree/A8TX70.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A8TX70/3_mltree/A8TX70.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A8TX70/3_mltree/A8TX70.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A8TX70/3_mltree/A8TX70.raxml.log Analysis started: 13-Jul-2021 17:32:17 / finished: 14-Jul-2021 15:18:27 Elapsed time: 78369.771 seconds Consumed energy: 4818.051 Wh (= 24 km in an electric car, or 120 km with an e-scooter!)