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 23-Jun-2021 00:32:40 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/O75173/2_msa/O75173_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/O75173/3_mltree/O75173.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/O75173/4_raxmlng_ancestral/O75173 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1624397560 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/030621_run/phylogeny-snakemake/results/O75173/2_msa/O75173_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 837 sites WARNING: Sequences tr_M3YTK7_M3YTK7_MUSPF_9669 and tr_E2QXE2_E2QXE2_CANLF_9615 are exactly identical! WARNING: Sequences tr_A0A2I2ZAM7_A0A2I2ZAM7_GORGO_9595 and tr_H2PAB9_H2PAB9_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2ZAM7_A0A2I2ZAM7_GORGO_9595 and tr_H2QMW5_H2QMW5_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2ZAM7_A0A2I2ZAM7_GORGO_9595 and sp_Q9P2N4_ATS9_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2ZAM7_A0A2I2ZAM7_GORGO_9595 and tr_A0A2R8ZXK3_A0A2R8ZXK3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QVR6_G3QVR6_GORGO_9595 and tr_K7C8I8_K7C8I8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QVR6_G3QVR6_GORGO_9595 and tr_A0A2R9BJM3_A0A2R9BJM3_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RJ61_G3RJ61_GORGO_9595 and tr_H2R5K7_H2R5K7_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RJ61_G3RJ61_GORGO_9595 and sp_Q9UKP5_ATS6_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QKW0_H2QKW0_PANTR_9598 and tr_A0A2R8Z755_A0A2R8Z755_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R0A6_H2R0A6_PANTR_9598 and tr_A0A2R9CI31_A0A2R9CI31_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5P8S1_W5P8S1_SHEEP_9940 and tr_E1BK03_E1BK03_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A1D5RKT0_A0A1D5RKT0_MACMU_9544 and tr_A0A2K6BRR0_A0A2K6BRR0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7ECB0_F7ECB0_MACMU_9544 and tr_A0A2K5N6E2_A0A2K5N6E2_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7ECB0_F7ECB0_MACMU_9544 and tr_A0A2K6BFE9_A0A2K6BFE9_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7ECB0_F7ECB0_MACMU_9544 and tr_A0A2K6A8S9_A0A2K6A8S9_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7H0I0_F7H0I0_MACMU_9544 and tr_A0A096NA48_A0A096NA48_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7H0I0_F7H0I0_MACMU_9544 and tr_A0A2K5ZK99_A0A2K5ZK99_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7ME94_G7ME94_MACMU_9544 and tr_A0A2K5XKM3_A0A2K5XKM3_MANLE_9568 are exactly identical! WARNING: Sequences tr_G8F2G2_G8F2G2_MACFA_9541 and tr_A0A2K6C5F5_A0A2K6C5F5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096N1C0_A0A096N1C0_PAPAN_9555 and tr_A0A2K6CKI8_A0A2K6CKI8_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0A0MVK0_A0A0A0MVK0_PAPAN_9555 and tr_A0A2K5MVF8_A0A2K5MVF8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0V1P068_A0A0V1P068_9BILA_92180 and tr_A0A0V0U132_A0A0V0U132_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A226MN07_A0A226MN07_CALSU_9009 and tr_A0A226PI57_A0A226PI57_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226MQ32_A0A226MQ32_CALSU_9009 and tr_A0A226PP34_A0A226PP34_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PKQ1_A0A2D0PKQ1_ICTPU_7998 and tr_A0A2D0PMG2_A0A2D0PMG2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RUX6_A0A2D0RUX6_ICTPU_7998 and tr_W5U8X9_W5U8X9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SFK5_A0A2D0SFK5_ICTPU_7998 and tr_A0A2D0SGV6_A0A2D0SGV6_ICTPU_7998 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/030621_run/phylogeny-snakemake/results/O75173/4_raxmlng_ancestral/O75173.raxml.reduced.phy Alignment comprises 1 partitions and 837 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 837 Gaps: 14.44 % Invariant sites: 1.91 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/O75173/4_raxmlng_ancestral/O75173.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/030621_run/phylogeny-snakemake/results/O75173/3_mltree/O75173.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 210 / 16800 [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: -255197.309369 [00:00:00 -255197.309369] Initial branch length optimization [00:00:02 -252614.516030] Model parameter optimization (eps = 0.100000) [00:00:41] Tree #1, final logLikelihood: -252357.893157 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.160942,0.153413) (0.169109,0.292934) (0.357287,0.793801) (0.312661,2.053843) 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/030621_run/phylogeny-snakemake/results/O75173/4_raxmlng_ancestral/O75173.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/O75173/4_raxmlng_ancestral/O75173.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/O75173/4_raxmlng_ancestral/O75173.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/030621_run/phylogeny-snakemake/results/O75173/4_raxmlng_ancestral/O75173.raxml.log Analysis started: 23-Jun-2021 00:32:40 / finished: 23-Jun-2021 00:33:29 Elapsed time: 49.304 seconds Consumed energy: 3.820 Wh