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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 01-Jul-2021 01:44:43 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q00887/2_msa/Q00887_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q00887/3_mltree/Q00887 --seed 2 --threads 6 --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 (6 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q00887/2_msa/Q00887_trimmed_msa.fasta [00:00:00] Loaded alignment with 585 taxa and 402 sites WARNING: Sequences tr_B4R186_B4R186_DROSI_7240 and tr_Q9VFU7_Q9VFU7_DROME_7227 are exactly identical! WARNING: Sequences tr_Q297Q6_Q297Q6_DROPS_46245 and tr_B4G2W0_B4G2W0_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A2I3S4T3_A0A2I3S4T3_PANTR_9598 and tr_A0A2I3SWG4_A0A2I3SWG4_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2QG24_H2QG24_PANTR_9598 and tr_A0A2R9BGU9_A0A2R9BGU9_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QGE4_H2QGE4_PANTR_9598 and tr_A0A2R9AIU6_A0A2R9AIU6_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R427_H2R427_PANTR_9598 and tr_A0A2R9C095_A0A2R9C095_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2RCB2_H2RCB2_PANTR_9598 and sp_Q2WEN9_CEA16_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2Y9P316_A0A2Y9P316_DELLE_9749 and tr_A0A2Y9P361_A0A2Y9P361_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 8 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/Q00887/3_mltree/Q00887.raxml.reduced.phy Alignment comprises 1 partitions and 402 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 402 / 402 Gaps: 29.91 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q00887/3_mltree/Q00887.raxml.rba Parallelization scheme autoconfig: 3 worker(s) x 2 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 585 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 201 / 16080 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -345672.950778] Initial branch length optimization [00:00:02 -291102.180027] Model parameter optimization (eps = 10.000000) [00:00:39 -289483.903015] AUTODETECT spr round 1 (radius: 5) [00:01:53 -226596.657477] AUTODETECT spr round 2 (radius: 10) [00:03:18 -175732.214469] AUTODETECT spr round 3 (radius: 15) [00:05:00 -157956.868859] AUTODETECT spr round 4 (radius: 20) [00:07:22 -152478.133322] AUTODETECT spr round 5 (radius: 25) [00:10:05 -151267.303512] SPR radius for FAST iterations: 25 (autodetect) [00:10:05 -151267.303512] Model parameter optimization (eps = 3.000000) [00:10:32 -150969.278698] FAST spr round 1 (radius: 25) [00:12:32 -139236.049405] FAST spr round 2 (radius: 25) [00:14:01 -138793.965372] FAST spr round 3 (radius: 25) [00:15:14 -138712.973152] FAST spr round 4 (radius: 25) [00:16:16 -138709.193333] FAST spr round 5 (radius: 25) [00:17:14 -138709.130436] Model parameter optimization (eps = 1.000000) [00:17:27 -138700.177617] SLOW spr round 1 (radius: 5) [00:19:03 -138671.082360] SLOW spr round 2 (radius: 5) [00:20:33 -138665.265046] SLOW spr round 3 (radius: 5) [00:21:58 -138665.260955] SLOW spr round 4 (radius: 10) [00:23:31 -138665.260750] SLOW spr round 5 (radius: 15) [00:26:53 -138665.260676] SLOW spr round 6 (radius: 20) [00:31:26 -138665.260608] SLOW spr round 7 (radius: 25) [00:36:34 -138665.260540] Model parameter optimization (eps = 0.100000) [00:36:39] [worker #0] ML tree search #1, logLikelihood: -138665.167494 [00:36:39 -345572.413283] Initial branch length optimization [00:36:42 -290641.941073] Model parameter optimization (eps = 10.000000) [00:37:15 -289046.840304] AUTODETECT spr round 1 (radius: 5) [00:38:29 -226155.703339] AUTODETECT spr round 2 (radius: 10) [00:38:32] [worker #1] ML tree search #2, logLikelihood: -138671.505276 [00:39:56 -181168.787496] AUTODETECT spr round 3 (radius: 15) [00:41:41 -160522.921646] AUTODETECT spr round 4 (radius: 20) [00:43:32] [worker #2] ML tree search #3, logLikelihood: -138638.636890 [00:43:59 -152548.931212] AUTODETECT spr round 5 (radius: 25) [00:47:07 -151883.777763] SPR radius for FAST iterations: 25 (autodetect) [00:47:07 -151883.777763] Model parameter optimization (eps = 3.000000) [00:47:32 -151560.202170] FAST spr round 1 (radius: 25) [00:49:32 -139621.663514] FAST spr round 2 (radius: 25) [00:51:01 -138835.221860] FAST spr round 3 (radius: 25) [00:52:20 -138730.266180] FAST spr round 4 (radius: 25) [00:53:27 -138700.262329] FAST spr round 5 (radius: 25) [00:54:26 -138700.260024] Model parameter optimization (eps = 1.000000) [00:54:44 -138684.829374] SLOW spr round 1 (radius: 5) [00:56:27 -138653.479268] SLOW spr round 2 (radius: 5) [00:57:58 -138649.441385] SLOW spr round 3 (radius: 5) [00:59:24 -138649.439184] SLOW spr round 4 (radius: 10) [01:00:59 -138649.439069] SLOW spr round 5 (radius: 15) [01:04:22 -138649.439061] SLOW spr round 6 (radius: 20) [01:08:59 -138649.439061] SLOW spr round 7 (radius: 25) [01:14:08 -138649.439060] Model parameter optimization (eps = 0.100000) [01:14:19] [worker #0] ML tree search #4, logLikelihood: -138649.185206 [01:14:20 -345093.894427] Initial branch length optimization [01:14:22 -291170.275508] Model parameter optimization (eps = 10.000000) [01:14:56 -289518.339274] AUTODETECT spr round 1 (radius: 5) [01:16:09 -228397.132747] AUTODETECT spr round 2 (radius: 10) [01:17:39 -176540.434556] AUTODETECT spr round 3 (radius: 15) [01:19:27 -158455.270820] AUTODETECT spr round 4 (radius: 20) [01:20:58] [worker #1] ML tree search #5, logLikelihood: -138657.736353 [01:21:51 -152603.734108] AUTODETECT spr round 5 (radius: 25) [01:21:51] [worker #2] ML tree search #6, logLikelihood: -138655.300316 [01:24:54 -151495.596835] SPR radius for FAST iterations: 25 (autodetect) [01:24:54 -151495.596835] Model parameter optimization (eps = 3.000000) [01:25:18 -151206.641791] FAST spr round 1 (radius: 25) [01:27:21 -139246.987383] FAST spr round 2 (radius: 25) [01:28:52 -138743.718229] FAST spr round 3 (radius: 25) [01:30:09 -138686.207025] FAST spr round 4 (radius: 25) [01:31:11 -138682.481613] FAST spr round 5 (radius: 25) [01:32:10 -138682.479442] Model parameter optimization (eps = 1.000000) [01:32:25 -138670.821989] SLOW spr round 1 (radius: 5) [01:34:03 -138649.849164] SLOW spr round 2 (radius: 5) [01:35:35 -138647.082203] SLOW spr round 3 (radius: 5) [01:37:01 -138646.991756] SLOW spr round 4 (radius: 10) [01:38:38 -138646.991668] SLOW spr round 5 (radius: 15) [01:42:10 -138646.991666] SLOW spr round 6 (radius: 20) [01:47:20 -138646.991666] SLOW spr round 7 (radius: 25) [01:53:08 -138646.991666] Model parameter optimization (eps = 0.100000) [01:53:21] [worker #0] ML tree search #7, logLikelihood: -138646.758076 [01:53:21 -345659.439562] Initial branch length optimization [01:53:24 -290505.005565] Model parameter optimization (eps = 10.000000) [01:54:02 -289039.521552] AUTODETECT spr round 1 (radius: 5) [01:55:17 -225162.252384] AUTODETECT spr round 2 (radius: 10) [01:56:46 -176636.085777] AUTODETECT spr round 3 (radius: 15) [01:58:37 -157208.100145] AUTODETECT spr round 4 (radius: 20) [02:01:06 -150929.723970] AUTODETECT spr round 5 (radius: 25) [02:04:02 -150881.058121] SPR radius for FAST iterations: 25 (autodetect) [02:04:02 -150881.058121] Model parameter optimization (eps = 3.000000) [02:04:24 -150541.919136] FAST spr round 1 (radius: 25) [02:06:23 -139308.713280] FAST spr round 2 (radius: 25) [02:07:55 -138771.408982] FAST spr round 3 (radius: 25) [02:09:16 -138729.249807] FAST spr round 4 (radius: 25) [02:09:24] [worker #1] ML tree search #8, logLikelihood: -138654.452642 [02:10:21 -138716.804582] FAST spr round 5 (radius: 25) [02:11:21 -138710.863835] FAST spr round 6 (radius: 25) [02:11:28] [worker #2] ML tree search #9, logLikelihood: -138665.282162 [02:12:19 -138710.863244] Model parameter optimization (eps = 1.000000) [02:12:32 -138706.260068] SLOW spr round 1 (radius: 5) [02:14:11 -138681.005339] SLOW spr round 2 (radius: 5) [02:15:43 -138676.991822] SLOW spr round 3 (radius: 5) [02:17:09 -138676.544612] SLOW spr round 4 (radius: 5) [02:18:34 -138676.544514] SLOW spr round 5 (radius: 10) [02:20:07 -138668.275243] SLOW spr round 6 (radius: 5) [02:22:02 -138665.617730] SLOW spr round 7 (radius: 5) [02:23:39 -138665.615421] SLOW spr round 8 (radius: 10) [02:25:16 -138665.615138] SLOW spr round 9 (radius: 15) [02:28:08 -138665.615101] SLOW spr round 10 (radius: 20) [02:32:16 -138665.615096] SLOW spr round 11 (radius: 25) [02:36:55 -138665.615095] Model parameter optimization (eps = 0.100000) [02:37:03] [worker #0] ML tree search #10, logLikelihood: -138665.332870 [02:37:03 -345005.417197] Initial branch length optimization [02:37:06 -289663.874832] Model parameter optimization (eps = 10.000000) [02:37:39 -288152.909853] AUTODETECT spr round 1 (radius: 5) [02:38:53 -230155.945282] AUTODETECT spr round 2 (radius: 10) [02:40:20 -178797.542266] AUTODETECT spr round 3 (radius: 15) [02:42:16 -157786.708052] AUTODETECT spr round 4 (radius: 20) [02:44:41 -152948.236075] AUTODETECT spr round 5 (radius: 25) [02:47:23 -152777.217910] SPR radius for FAST iterations: 25 (autodetect) [02:47:23 -152777.217910] Model parameter optimization (eps = 3.000000) [02:47:46 -152476.515834] FAST spr round 1 (radius: 25) [02:49:47 -139686.414766] FAST spr round 2 (radius: 25) [02:51:15 -138816.619134] FAST spr round 3 (radius: 25) [02:52:30 -138758.243332] FAST spr round 4 (radius: 25) [02:53:35 -138745.923082] FAST spr round 5 (radius: 25) [02:54:32 -138745.921438] Model parameter optimization (eps = 1.000000) [02:54:59 -138727.497987] SLOW spr round 1 (radius: 5) [02:56:36 -138689.178721] SLOW spr round 2 (radius: 5) [02:57:15] [worker #1] ML tree search #11, logLikelihood: -138665.099772 [02:58:04 -138687.097736] SLOW spr round 3 (radius: 5) [02:59:29 -138687.097484] SLOW spr round 4 (radius: 10) [03:00:26] [worker #2] ML tree search #12, logLikelihood: -138648.646037 [03:01:08 -138680.132948] SLOW spr round 5 (radius: 5) [03:03:10 -138657.178633] SLOW spr round 6 (radius: 5) [03:04:49 -138648.209969] SLOW spr round 7 (radius: 5) [03:06:20 -138647.850645] SLOW spr round 8 (radius: 5) [03:07:46 -138647.850411] SLOW spr round 9 (radius: 10) [03:09:20 -138647.850317] SLOW spr round 10 (radius: 15) [03:12:52 -138647.850239] SLOW spr round 11 (radius: 20) [03:18:05 -138647.850163] SLOW spr round 12 (radius: 25) [03:23:56 -138647.850087] Model parameter optimization (eps = 0.100000) [03:24:06] [worker #0] ML tree search #13, logLikelihood: -138646.944908 [03:24:06 -344153.932353] Initial branch length optimization [03:24:09 -289109.263307] Model parameter optimization (eps = 10.000000) [03:24:37 -287582.806854] AUTODETECT spr round 1 (radius: 5) [03:25:51 -230185.069333] AUTODETECT spr round 2 (radius: 10) [03:27:18 -176917.044589] AUTODETECT spr round 3 (radius: 15) [03:29:03 -160101.776612] AUTODETECT spr round 4 (radius: 20) [03:31:00 -154314.836002] AUTODETECT spr round 5 (radius: 25) [03:33:20 -151979.436888] SPR radius for FAST iterations: 25 (autodetect) [03:33:20 -151979.436888] Model parameter optimization (eps = 3.000000) [03:33:40 -151679.934353] FAST spr round 1 (radius: 25) [03:35:46 -139408.142137] FAST spr round 2 (radius: 25) [03:35:49] [worker #2] ML tree search #15, logLikelihood: -138651.439975 [03:37:14 -138816.382209] FAST spr round 3 (radius: 25) [03:38:30 -138783.202932] FAST spr round 4 (radius: 25) [03:39:33 -138768.556822] FAST spr round 5 (radius: 25) [03:40:36 -138752.698333] FAST spr round 6 (radius: 25) [03:41:09] [worker #1] ML tree search #14, logLikelihood: -138651.863895 [03:41:35 -138745.874599] FAST spr round 7 (radius: 25) [03:42:32 -138745.873608] Model parameter optimization (eps = 1.000000) [03:42:49 -138717.956037] SLOW spr round 1 (radius: 5) [03:44:29 -138677.726068] SLOW spr round 2 (radius: 5) [03:45:55 -138677.559752] SLOW spr round 3 (radius: 5) [03:47:19 -138677.559728] SLOW spr round 4 (radius: 10) [03:48:52 -138676.344614] SLOW spr round 5 (radius: 5) [03:50:44 -138676.344606] SLOW spr round 6 (radius: 10) [03:52:32 -138676.344605] SLOW spr round 7 (radius: 15) [03:55:22 -138676.344605] SLOW spr round 8 (radius: 20) [03:59:44 -138676.344605] SLOW spr round 9 (radius: 25) [04:04:43 -138676.344604] Model parameter optimization (eps = 0.100000) [04:04:52] [worker #0] ML tree search #16, logLikelihood: -138676.231989 [04:04:52 -345841.803419] Initial branch length optimization [04:04:54 -290455.360437] Model parameter optimization (eps = 10.000000) [04:05:34 -288871.434180] AUTODETECT spr round 1 (radius: 5) [04:06:46 -231317.159692] AUTODETECT spr round 2 (radius: 10) [04:08:14 -177868.775462] AUTODETECT spr round 3 (radius: 15) [04:10:07 -160099.576472] AUTODETECT spr round 4 (radius: 20) [04:12:38 -153355.698690] AUTODETECT spr round 5 (radius: 25) [04:15:30 -152752.014124] SPR radius for FAST iterations: 25 (autodetect) [04:15:30 -152752.014124] Model parameter optimization (eps = 3.000000) [04:15:56 -152419.028524] FAST spr round 1 (radius: 25) [04:17:52 -139347.074511] FAST spr round 2 (radius: 25) [04:19:13] [worker #1] ML tree search #17, logLikelihood: -138666.314530 [04:19:19 -138780.695694] FAST spr round 3 (radius: 25) [04:20:37 -138725.471177] FAST spr round 4 (radius: 25) [04:21:46 -138708.455692] FAST spr round 5 (radius: 25) [04:22:38] [worker #2] ML tree search #18, logLikelihood: -138643.966796 [04:22:48 -138703.535166] FAST spr round 6 (radius: 25) [04:23:49 -138701.099968] FAST spr round 7 (radius: 25) [04:24:45 -138701.099819] Model parameter optimization (eps = 1.000000) [04:24:59 -138684.078292] SLOW spr round 1 (radius: 5) [04:26:36 -138655.455720] SLOW spr round 2 (radius: 5) [04:28:03 -138651.732289] SLOW spr round 3 (radius: 5) [04:29:26 -138651.732249] SLOW spr round 4 (radius: 10) [04:30:58 -138650.754600] SLOW spr round 5 (radius: 5) [04:32:51 -138644.229776] SLOW spr round 6 (radius: 5) [04:34:26 -138644.229775] SLOW spr round 7 (radius: 10) [04:36:05 -138644.123375] SLOW spr round 8 (radius: 5) [04:37:58 -138642.612215] SLOW spr round 9 (radius: 5) [04:39:33 -138642.612076] SLOW spr round 10 (radius: 10) [04:41:11 -138642.612051] SLOW spr round 11 (radius: 15) [04:44:24 -138642.612035] SLOW spr round 12 (radius: 20) [04:49:05 -138642.612024] SLOW spr round 13 (radius: 25) [04:54:23 -138642.612014] Model parameter optimization (eps = 0.100000) [04:54:29] [worker #0] ML tree search #19, logLikelihood: -138642.545664 [05:04:30] [worker #1] ML tree search #20, logLikelihood: -138636.526639 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.127941,0.650669) (0.060392,0.503917) (0.492532,0.864515) (0.319135,1.443022) 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: -138636.526639 AIC score: 279619.053278 / AICc score: 3033823.053278 / BIC score: 284306.891578 Free parameters (model + branch lengths): 1173 WARNING: Number of free parameters (K=1173) is larger than alignment size (n=402). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 16 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q00887/3_mltree/Q00887.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q00887/3_mltree/Q00887.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q00887/3_mltree/Q00887.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q00887/3_mltree/Q00887.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q00887/3_mltree/Q00887.raxml.log Analysis started: 01-Jul-2021 01:44:43 / finished: 01-Jul-2021 06:49:14 Elapsed time: 18270.616 seconds Consumed energy: 936.396 Wh (= 5 km in an electric car, or 23 km with an e-scooter!)