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 17:22:53 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6NZ63/2_msa/Q6NZ63_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6NZ63/3_mltree/Q6NZ63.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6NZ63/4_raxmlng_ancestral/Q6NZ63 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626099773 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/Q6NZ63/2_msa/Q6NZ63_nogap_msa.fasta [00:00:00] Loaded alignment with 419 taxa and 245 sites WARNING: Sequences tr_A0A2I2ZM14_A0A2I2ZM14_GORGO_9595 and tr_A0A2I3T4J7_A0A2I3T4J7_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2ZM14_A0A2I2ZM14_GORGO_9595 and tr_K7DAA1_K7DAA1_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2ZM14_A0A2I2ZM14_GORGO_9595 and tr_A0A2R8ZDU2_A0A2R8ZDU2_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RBZ6_G3RBZ6_GORGO_9595 and sp_Q687X5_STEA4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2R574_H2R574_PANTR_9598 and tr_A0A2R9ANB7_A0A2R9ANB7_PANPA_9597 are exactly identical! WARNING: Sequences tr_K6ZGM4_K6ZGM4_PANTR_9598 and tr_A0A2R9A6Q7_A0A2R9A6Q7_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7AVA0_F7AVA0_MONDO_13616 and tr_F7DT80_F7DT80_MONDO_13616 are exactly identical! WARNING: Sequences tr_W5PGZ3_W5PGZ3_SHEEP_9940 and tr_W5PQQ1_W5PQQ1_SHEEP_9940 are exactly identical! WARNING: Sequences tr_W5PQR1_W5PQR1_SHEEP_9940 and tr_F1S336_F1S336_PIG_9823 are exactly identical! WARNING: Sequences tr_W5PQR1_W5PQR1_SHEEP_9940 and tr_A0JNK9_A0JNK9_BOVIN_9913 are exactly identical! WARNING: Sequences tr_F6PLK4_F6PLK4_MACMU_9544 and tr_B0CM24_B0CM24_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6PLK4_F6PLK4_MACMU_9544 and tr_A0A0D9RJ61_A0A0D9RJ61_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7HSI7_F7HSI7_MACMU_9544 and tr_G7PN50_G7PN50_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7HSI7_F7HSI7_MACMU_9544 and tr_A0A2I3LP23_A0A2I3LP23_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HSI7_F7HSI7_MACMU_9544 and tr_A0A0D9RVI4_A0A0D9RVI4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7HSI7_F7HSI7_MACMU_9544 and tr_A0A2K5N870_A0A2K5N870_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HSI7_F7HSI7_MACMU_9544 and tr_A0A2K6CSC7_A0A2K6CSC7_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HSI7_F7HSI7_MACMU_9544 and tr_A0A2K5ZH84_A0A2K5ZH84_MANLE_9568 are exactly identical! WARNING: Sequences tr_D2HE08_D2HE08_AILME_9646 and tr_A0A2Y9JMN2_A0A2Y9JMN2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_D2HE08_D2HE08_AILME_9646 and tr_A0A384BPD8_A0A384BPD8_URSMA_29073 are exactly identical! WARNING: Sequences tr_G7P1U9_G7P1U9_MACFA_9541 and tr_A0A2K5LUP2_A0A2K5LUP2_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7P1U9_G7P1U9_MACFA_9541 and tr_A0A2K6BA74_A0A2K6BA74_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7P1U9_G7P1U9_MACFA_9541 and tr_A0A2K6AJE9_A0A2K6AJE9_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7P1V2_G7P1V2_MACFA_9541 and tr_A0A0D9RJ46_A0A0D9RJ46_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7P1V2_G7P1V2_MACFA_9541 and tr_A0A2K6CLE0_A0A2K6CLE0_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7P1V2_G7P1V2_MACFA_9541 and tr_A0A2K5ZGQ7_A0A2K5ZGQ7_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A091V6D0_A0A091V6D0_NIPNI_128390 and tr_A0A091WA82_A0A091WA82_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A226MTQ3_A0A226MTQ3_CALSU_9009 and tr_A0A226P0M8_A0A226P0M8_COLVI_9014 are exactly identical! WARNING: Duplicate sequences found: 28 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/Q6NZ63/4_raxmlng_ancestral/Q6NZ63.raxml.reduced.phy Alignment comprises 1 partitions and 245 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 245 Gaps: 3.30 % Invariant sites: 2.04 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6NZ63/4_raxmlng_ancestral/Q6NZ63.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/Q6NZ63/3_mltree/Q6NZ63.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 62 / 4960 [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: -38148.912757 [00:00:00 -38148.912757] Initial branch length optimization [00:00:00 -37895.743167] Model parameter optimization (eps = 0.100000) [00:00:18] Tree #1, final logLikelihood: -37621.331147 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.259321,0.641410) (0.233619,1.194553) (0.379716,0.823823) (0.127343,1.898643) 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/Q6NZ63/4_raxmlng_ancestral/Q6NZ63.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6NZ63/4_raxmlng_ancestral/Q6NZ63.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6NZ63/4_raxmlng_ancestral/Q6NZ63.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6NZ63/4_raxmlng_ancestral/Q6NZ63.raxml.log Analysis started: 12-Jul-2021 17:22:53 / finished: 12-Jul-2021 17:23:12 Elapsed time: 19.049 seconds Consumed energy: 1.459 Wh