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 12-Jul-2021 17:37:33 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35125/2_msa/P35125_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35125/3_mltree/P35125.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35125/4_raxmlng_ancestral/P35125 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626100653 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/P35125/2_msa/P35125_nogap_msa.fasta [00:00:00] Loaded alignment with 981 taxa and 1406 sites WARNING: Sequences tr_M3YZ48_M3YZ48_MUSPF_9669 and tr_A0A2Y9KXD2_A0A2Y9KXD2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1S5L1_G1S5L1_NOMLE_61853 and tr_G3QJX5_G3QJX5_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S5L1_G1S5L1_NOMLE_61853 and tr_K7ETJ3_K7ETJ3_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1S5L1_G1S5L1_NOMLE_61853 and tr_A0A2I3S9E9_A0A2I3S9E9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S5L1_G1S5L1_NOMLE_61853 and sp_Q9Y4E8_UBP15_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1S5L1_G1S5L1_NOMLE_61853 and tr_F6QY64_F6QY64_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1S5L1_G1S5L1_NOMLE_61853 and tr_G7PIX8_G7PIX8_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1S5L1_G1S5L1_NOMLE_61853 and tr_A0A096MWR8_A0A096MWR8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1S5L1_G1S5L1_NOMLE_61853 and tr_A0A0D9QWY1_A0A0D9QWY1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1S5L1_G1S5L1_NOMLE_61853 and tr_A0A2K5KSW7_A0A2K5KSW7_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1S5L1_G1S5L1_NOMLE_61853 and tr_A0A2K6CCL5_A0A2K6CCL5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1S5L1_G1S5L1_NOMLE_61853 and tr_A0A2K5Z615_A0A2K5Z615_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1S5L1_G1S5L1_NOMLE_61853 and tr_A0A2R8Z6S5_A0A2R8Z6S5_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3SEY8_A0A2I3SEY8_PANTR_9598 and tr_A0A2R9BFS6_A0A2R9BFS6_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QML3_H2QML3_PANTR_9598 and tr_A0A2R9ADB3_A0A2R9ADB3_PANPA_9597 are exactly identical! WARNING: Sequences sp_A0A087WVF3_TBC3D_HUMAN_9606 and sp_A6NER0_TBC3F_HUMAN_9606 are exactly identical! WARNING: Sequences sp_A0A087WVF3_TBC3D_HUMAN_9606 and sp_Q6IPX1_TBC3C_HUMAN_9606 are exactly identical! WARNING: Sequences sp_A0A087WVF3_TBC3D_HUMAN_9606 and sp_Q8IZP1_TBC3A_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P0C7X1_TBC3H_HUMAN_9606 and sp_Q6DHY5_TBC3G_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A0E0G9H8_A0A0E0G9H8_ORYNI_4536 and tr_B8BN24_B8BN24_ORYSI_39946 are exactly identical! WARNING: Sequences tr_B8B7E9_B8B7E9_ORYSI_39946 and tr_A0A0P0X2E4_A0A0P0X2E4_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1Q875_I1Q875_ORYGL_4538 and tr_A0A0D3GMH2_A0A0D3GMH2_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_W2QF43_W2QF43_PHYPN_761204 and tr_W2LK73_W2LK73_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A096NC65_A0A096NC65_PAPAN_9555 and tr_A0A2K5XYX0_A0A2K5XYX0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3MIS9_A0A2I3MIS9_PAPAN_9555 and tr_A0A2K5NJ23_A0A2K5NJ23_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MIS9_A0A2I3MIS9_PAPAN_9555 and tr_A0A2K6BYJ1_A0A2K6BYJ1_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3N6R8_A0A2I3N6R8_PAPAN_9555 and tr_A0A2K6DQG7_A0A2K6DQG7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0A1N446_A0A0A1N446_9FUNG_58291 and tr_A0A367K8N4_A0A367K8N4_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A1D1VJ66_A0A1D1VJ66_RAMVA_947166 and tr_A0A1D1VPL0_A0A1D1VPL0_RAMVA_947166 are exactly identical! WARNING: Sequences tr_A0A2D0T466_A0A2D0T466_ICTPU_7998 and tr_A0A2D0T513_A0A2D0T513_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/300621_run/phylogeny-snakemake/results/P35125/4_raxmlng_ancestral/P35125.raxml.reduced.phy Alignment comprises 1 partitions and 1406 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1406 Gaps: 52.33 % Invariant sites: 0.78 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35125/4_raxmlng_ancestral/P35125.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/P35125/3_mltree/P35125.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 352 / 28160 [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: -775048.205834 [00:00:00 -775048.205834] Initial branch length optimization [00:00:05 -429219.119266] Model parameter optimization (eps = 0.100000) [00:01:14] Tree #1, final logLikelihood: -428363.425777 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.118042,0.277908) (0.128183,0.408718) (0.346129,0.733450) (0.407646,1.621350) 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/P35125/4_raxmlng_ancestral/P35125.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35125/4_raxmlng_ancestral/P35125.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35125/4_raxmlng_ancestral/P35125.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P35125/4_raxmlng_ancestral/P35125.raxml.log Analysis started: 12-Jul-2021 17:37:33 / finished: 12-Jul-2021 17:39:01 Elapsed time: 87.327 seconds Consumed energy: 7.115 Wh