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 12-Jul-2021 17:15:42 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08575/2_msa/P08575_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08575/3_mltree/P08575.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08575/4_raxmlng_ancestral/P08575 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626099342 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/300621_run/phylogeny-snakemake/results/P08575/2_msa/P08575_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1306 sites WARNING: Sequences tr_M3YTU5_M3YTU5_MUSPF_9669 and tr_A0A337RYS5_A0A337RYS5_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YTU5_M3YTU5_MUSPF_9669 and tr_A0A384BZR4_A0A384BZR4_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2I3GK79_A0A2I3GK79_NOMLE_61853 and tr_H2NBZ5_H2NBZ5_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I3GK79_A0A2I3GK79_NOMLE_61853 and tr_H2R3E7_H2R3E7_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3GK79_A0A2I3GK79_NOMLE_61853 and tr_A0A2R8ZB11_A0A2R8ZB11_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1R5I4_G1R5I4_NOMLE_61853 and sp_P28827_PTPRM_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2YGJ3_A0A2I2YGJ3_GORGO_9595 and tr_H2R1K1_H2R1K1_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YGJ3_A0A2I2YGJ3_GORGO_9595 and tr_A0A2R9B7Y1_A0A2R9B7Y1_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2RBP7_H2RBP7_PANTR_9598 and sp_P18433_PTPRA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2RBP7_H2RBP7_PANTR_9598 and tr_A0A2K5KVH8_A0A2K5KVH8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5Q4R1_A0A1D5Q4R1_MACMU_9544 and tr_A0A0D9RYA9_A0A0D9RYA9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6TLA3_F6TLA3_MACMU_9544 and tr_A0A2I3NAL0_A0A2I3NAL0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7DWH2_F7DWH2_MACMU_9544 and tr_G7PSD1_G7PSD1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HG97_F7HG97_MACMU_9544 and tr_A0A2I3LET0_A0A2I3LET0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1LLN7_G1LLN7_AILME_9646 and tr_A0A384C7G9_A0A384C7G9_URSMA_29073 are exactly identical! WARNING: Sequences tr_G7PEC8_G7PEC8_MACFA_9541 and tr_A0A2K6BYF7_A0A2K6BYF7_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PWE3_G7PWE3_MACFA_9541 and tr_A0A2K5LED7_A0A2K5LED7_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PWE3_G7PWE3_MACFA_9541 and tr_A0A2K6C632_A0A2K6C632_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096N7E0_A0A096N7E0_PAPAN_9555 and tr_A0A2K5Y7Q0_A0A2K5Y7Q0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3N9W3_A0A2I3N9W3_PAPAN_9555 and tr_A0A0D9R9K5_A0A0D9R9K5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3N9W3_A0A2I3N9W3_PAPAN_9555 and tr_A0A2K6A4P9_A0A2K6A4P9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0D9QWP4_A0A0D9QWP4_CHLSB_60711 and tr_A0A2K5LWU5_A0A2K5LWU5_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A091VX05_A0A091VX05_OPIHO_30419 and tr_A0A091G8Y5_A0A091G8Y5_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A195BU66_A0A195BU66_9HYME_520822 and tr_A0A195F635_A0A195F635_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A1S3HQ57_A0A1S3HQ57_LINUN_7574 and tr_A0A1S3HRJ8_A0A1S3HRJ8_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A226NB73_A0A226NB73_CALSU_9009 and tr_A0A226P275_A0A226P275_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0QEJ7_A0A2D0QEJ7_ICTPU_7998 and tr_A0A2D0QFL7_A0A2D0QFL7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QEJ7_A0A2D0QEJ7_ICTPU_7998 and tr_A0A2D0QFM4_A0A2D0QFM4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QEJ7_A0A2D0QEJ7_ICTPU_7998 and tr_A0A2D0QH24_A0A2D0QH24_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RUP4_A0A2D0RUP4_ICTPU_7998 and tr_W5UBA6_W5UBA6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RWZ5_A0A2D0RWZ5_ICTPU_7998 and tr_A0A2D0RXW6_A0A2D0RXW6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T9D0_A0A2D0T9D0_ICTPU_7998 and tr_A0A2D0T9D3_A0A2D0T9D3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T9D0_A0A2D0T9D0_ICTPU_7998 and tr_A0A2D0TA03_A0A2D0TA03_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4CLD7_A0A2U4CLD7_TURTR_9739 and tr_A0A2Y9PNW4_A0A2Y9PNW4_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CLD7_A0A2U4CLD7_TURTR_9739 and tr_A0A384B8A1_A0A384B8A1_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 35 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/P08575/4_raxmlng_ancestral/P08575.raxml.reduced.phy Alignment comprises 1 partitions and 1306 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1306 Gaps: 31.59 % Invariant sites: 0.23 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08575/4_raxmlng_ancestral/P08575.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/300621_run/phylogeny-snakemake/results/P08575/3_mltree/P08575.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 327 / 26160 [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: -353414.225282 [00:00:00 -353414.225282] Initial branch length optimization [00:00:02 -330263.741178] Model parameter optimization (eps = 0.100000) [00:01:27] Tree #1, final logLikelihood: -329432.023858 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.147768,0.276068) (0.148907,0.340927) (0.391040,0.755704) (0.312285,1.962721) 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/300621_run/phylogeny-snakemake/results/P08575/4_raxmlng_ancestral/P08575.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08575/4_raxmlng_ancestral/P08575.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08575/4_raxmlng_ancestral/P08575.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P08575/4_raxmlng_ancestral/P08575.raxml.log Analysis started: 12-Jul-2021 17:15:42 / finished: 12-Jul-2021 17:17:22 Elapsed time: 100.471 seconds Consumed energy: 5.859 Wh