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 03-Jun-2021 02:24:55 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96NR8/2_msa/Q96NR8_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96NR8/3_mltree/Q96NR8.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96NR8/4_raxmlng_ancestral/Q96NR8 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622676295 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/Q96NR8/2_msa/Q96NR8_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 316 sites WARNING: Sequences tr_M3YQE7_M3YQE7_MUSPF_9669 and tr_A0A2Y9K6K1_A0A2Y9K6K1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G3QDX2_G3QDX2_GORGO_9595 and sp_Q8NBN7_RDH13_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3S1Z2_G3S1Z2_GORGO_9595 and tr_K7CS04_K7CS04_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3S1Z2_G3S1Z2_GORGO_9595 and sp_Q6UX07_DHR13_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8WM62_A0A2J8WM62_PONAB_9601 and tr_A0A2J8PIT4_A0A2J8PIT4_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2J8WM62_A0A2J8WM62_PONAB_9601 and sp_Q96NR8_RDH12_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8WM62_A0A2J8WM62_PONAB_9601 and tr_A0A2R9C7Y4_A0A2R9C7Y4_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2NRJ9_H2NRJ9_PONAB_9601 and sp_Q5R9W5_WWOX_PONAB_9601 are exactly identical! WARNING: Sequences tr_H2QH50_H2QH50_PANTR_9598 and tr_A0A2R8ZJY5_A0A2R8ZJY5_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q8TC12_RDH11_HUMAN_9606 and tr_A0A2R9BIG4_A0A2R9BIG4_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0E0FGA6_A0A0E0FGA6_ORYNI_4536 and tr_A0A0E0MRE9_A0A0E0MRE9_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0FGA6_A0A0E0FGA6_ORYNI_4536 and tr_Q9LGI8_Q9LGI8_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_F7C217_F7C217_MACMU_9544 and tr_A0A096NVQ8_A0A096NVQ8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7C217_F7C217_MACMU_9544 and tr_A0A0D9RLD1_A0A0D9RLD1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7C217_F7C217_MACMU_9544 and tr_A0A2K5NL50_A0A2K5NL50_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7C217_F7C217_MACMU_9544 and tr_A0A2K6B3D9_A0A2K6B3D9_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7C217_F7C217_MACMU_9544 and tr_A0A2K5YL47_A0A2K5YL47_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7C225_F7C225_MACMU_9544 and tr_Q4JK72_Q4JK72_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7C225_F7C225_MACMU_9544 and tr_A0A2K6DZ12_A0A2K6DZ12_MACNE_9545 are exactly identical! WARNING: Sequences tr_B8BJF9_B8BJF9_ORYSI_39946 and tr_A0A0E0R4Z9_A0A0E0R4Z9_ORYRU_4529 are exactly identical! WARNING: Sequences tr_B8BJF9_B8BJF9_ORYSI_39946 and tr_Q0IU69_Q0IU69_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1QY90_I1QY90_ORYGL_4538 and tr_Q53ML7_Q53ML7_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_B3RKN6_B3RKN6_TRIAD_10228 and tr_A0A369RXE5_A0A369RXE5_9METZ_287889 are exactly identical! WARNING: Sequences tr_B3RZ14_B3RZ14_TRIAD_10228 and tr_A0A369RRU1_A0A369RRU1_9METZ_287889 are exactly identical! WARNING: Sequences tr_B3SEC8_B3SEC8_TRIAD_10228 and tr_A0A369RLX1_A0A369RLX1_9METZ_287889 are exactly identical! WARNING: Sequences tr_A0A096P3F3_A0A096P3F3_PAPAN_9555 and tr_A0A0D9R420_A0A0D9R420_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096P3F3_A0A096P3F3_PAPAN_9555 and tr_A0A2K5LDW9_A0A2K5LDW9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096P3F3_A0A096P3F3_PAPAN_9555 and tr_A0A2K6BCR5_A0A2K6BCR5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1S4A5D4_A0A1S4A5D4_TOBAC_4097 and tr_A0A1U7VAC6_A0A1U7VAC6_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4BLZ3_A0A1S4BLZ3_TOBAC_4097 and tr_A0A1U7WRU2_A0A1U7WRU2_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2D0RRH5_A0A2D0RRH5_ICTPU_7998 and tr_W5U966_W5U966_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A1U8E748_A0A1U8E748_CAPAN_4072 and tr_A0A2G3BF56_A0A2G3BF56_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2U4APM8_A0A2U4APM8_TURTR_9739 and tr_A0A2U4APN1_A0A2U4APN1_TURTR_9739 are exactly identical! WARNING: Duplicate sequences found: 33 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/Q96NR8/4_raxmlng_ancestral/Q96NR8.raxml.reduced.phy Alignment comprises 1 partitions and 316 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 316 Gaps: 7.03 % Invariant sites: 0.63 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96NR8/4_raxmlng_ancestral/Q96NR8.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/Q96NR8/3_mltree/Q96NR8.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 79 / 6320 [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: -192890.326889 [00:00:00 -192890.326889] Initial branch length optimization [00:00:01 -192341.024464] Model parameter optimization (eps = 0.100000) [00:00:26] Tree #1, final logLikelihood: -191766.356056 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.198308,0.308999) (0.207530,0.357845) (0.328672,0.988797) (0.265491,2.031972) 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/Q96NR8/4_raxmlng_ancestral/Q96NR8.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96NR8/4_raxmlng_ancestral/Q96NR8.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96NR8/4_raxmlng_ancestral/Q96NR8.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q96NR8/4_raxmlng_ancestral/Q96NR8.raxml.log Analysis started: 03-Jun-2021 02:24:55 / finished: 03-Jun-2021 02:25:25 Elapsed time: 29.599 seconds Consumed energy: 1.734 Wh