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 02-Jun-2021 18:08:56 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14164/2_msa/Q14164_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14164/3_mltree/Q14164.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14164/4_raxmlng_ancestral/Q14164 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622646536 tip-inner: ON pattern compression: OFF per-rate scalers: OFF site repeats: OFF branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14164/2_msa/Q14164_nogap_msa.fasta [00:00:00] Loaded alignment with 998 taxa and 716 sites WARNING: Sequences sp_Q8CIP4_MARK4_MOUSE_10090 and tr_D4A6T9_D4A6T9_RAT_10116 are exactly identical! WARNING: Sequences tr_A0A2I2Z864_A0A2I2Z864_GORGO_9595 and tr_K7ARJ8_K7ARJ8_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2Q6E2_H2Q6E2_PANTR_9598 and tr_A0A2R8ZIM2_A0A2R8ZIM2_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QL36_H2QL36_PANTR_9598 and sp_Q96L34_MARK4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QL36_H2QL36_PANTR_9598 and tr_A0A2R9AJS8_A0A2R9AJS8_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7C5W4_K7C5W4_PANTR_9598 and sp_Q14164_IKKE_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7DNJ5_K7DNJ5_PANTR_9598 and sp_Q9NRP7_STK36_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A088APZ5_A0A088APZ5_APIME_7460 and tr_A0A2A3EIA7_A0A2A3EIA7_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NI20_A0A158NI20_ATTCE_12957 and tr_A0A151I4C2_A0A151I4C2_9HYME_520822 are exactly identical! WARNING: Sequences tr_I3MHI3_I3MHI3_ICTTR_43179 and tr_A0A2I3LQ00_A0A2I3LQ00_PAPAN_9555 are exactly identical! WARNING: Sequences tr_I3MHI3_I3MHI3_ICTTR_43179 and tr_A0A2K5P6P7_A0A2K5P6P7_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7DBZ3_F7DBZ3_MACMU_9544 and tr_A0A096MZ73_A0A096MZ73_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7DBZ3_F7DBZ3_MACMU_9544 and tr_A0A2K6DYC3_A0A2K6DYC3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7DBZ3_F7DBZ3_MACMU_9544 and tr_A0A2K5Z5D5_A0A2K5Z5D5_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7HD33_F7HD33_MACMU_9544 and tr_G7P2C9_G7P2C9_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HD33_F7HD33_MACMU_9544 and tr_A0A2K5YUA2_A0A2K5YUA2_MANLE_9568 are exactly identical! WARNING: Sequences tr_H9EV28_H9EV28_MACMU_9544 and tr_A0A096P352_A0A096P352_PAPAN_9555 are exactly identical! WARNING: Sequences tr_B8AKP1_B8AKP1_ORYSI_39946 and tr_I1P9V3_I1P9V3_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A287BEB6_A0A287BEB6_PIG_9823 and tr_A0A2U3VZL2_A0A2U3VZL2_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A287BEB6_A0A287BEB6_PIG_9823 and tr_A0A2U3Y4F3_A0A2U3Y4F3_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A287BEB6_A0A287BEB6_PIG_9823 and tr_A0A2Y9L1K0_A0A2Y9L1K0_ENHLU_391180 are exactly identical! WARNING: Sequences tr_W2Q5T6_W2Q5T6_PHYPN_761204 and tr_A0A0W8C117_A0A0W8C117_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2Q5T6_W2Q5T6_PHYPN_761204 and tr_W2L5V5_W2L5V5_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2RJX7_W2RJX7_PHYPN_761204 and tr_A0A0W8D448_A0A0W8D448_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A0A1P849_A0A0A1P849_9FUNG_58291 and tr_A0A367K7D6_A0A367K7D6_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A091FV46_A0A091FV46_9AVES_55661 and tr_A0A0A0AEH7_A0A0A0AEH7_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2I0LYP9_A0A2I0LYP9_COLLI_8932 and tr_A0A1V4K251_A0A1V4K251_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1S4DI99_A0A1S4DI99_TOBAC_4097 and tr_A0A1U7VQY5_A0A1U7VQY5_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3V7Y3_A0A1S3V7Y3_VIGRR_3916 and tr_A0A3Q0F995_A0A3Q0F995_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A2D0T0A7_A0A2D0T0A7_ICTPU_7998 and tr_W5UIG3_W5UIG3_ICTPU_7998 are exactly identical! WARNING: Duplicate sequences found: 30 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14164/4_raxmlng_ancestral/Q14164.raxml.reduced.phy Alignment comprises 1 partitions and 716 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 716 Gaps: 33.05 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14164/4_raxmlng_ancestral/Q14164.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 4 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Loading user starting tree(s) from: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14164/3_mltree/Q14164.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 179 / 14320 [00:00:00] Data distribution: max. searches per worker: 1 Starting ML tree search with 1 distinct starting trees [00:00:00] Tree #1, initial LogLikelihood: -347202.022176 [00:00:00 -347202.022176] Initial branch length optimization [00:00:04 -318809.868665] Model parameter optimization (eps = 0.100000) [00:02:01] Tree #1, final logLikelihood: -317887.215253 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.073309,0.197149) (0.120719,0.233886) (0.440238,0.809499) (0.365734,1.643108) 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 Marginal ancestral probabilities saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14164/4_raxmlng_ancestral/Q14164.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14164/4_raxmlng_ancestral/Q14164.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14164/4_raxmlng_ancestral/Q14164.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q14164/4_raxmlng_ancestral/Q14164.raxml.log Analysis started: 02-Jun-2021 18:08:56 / finished: 02-Jun-2021 18:11:05 Elapsed time: 129.106 seconds Consumed energy: 11.520 Wh