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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 04-Jun-2021 14:17:44 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P21757/2_msa/P21757_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P21757/3_mltree/P21757.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P21757/4_raxmlng_ancestral/P21757 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622805464 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P21757/2_msa/P21757_nogap_msa.fasta [00:00:00] Loaded alignment with 963 taxa and 451 sites WARNING: Sequences tr_A0A2R8QAP7_A0A2R8QAP7_DANRE_7955 and tr_F1QM24_F1QM24_DANRE_7955 are exactly identical! WARNING: Sequences tr_G3QK11_G3QK11_GORGO_9595 and sp_Q5G270_NETR_GORGO_9595 are exactly identical! WARNING: Sequences tr_F1PL60_F1PL60_CANLF_9615 and sp_Q2VLG6_C163A_CANLF_9615 are exactly identical! WARNING: Sequences tr_A0A2I3TAV9_A0A2I3TAV9_PANTR_9598 and tr_A0A2R9B9G2_A0A2R9B9G2_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3TET7_A0A2I3TET7_PANTR_9598 and tr_A0A2R9BMI0_A0A2R9BMI0_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q5G271_NETR_PANTR_9598 and sp_P56730_NETR_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q5G271_NETR_PANTR_9598 and tr_A0A2R9B643_A0A2R9B643_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5Q5F6_A0A1D5Q5F6_MACMU_9544 and tr_G7PCC1_G7PCC1_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5Q5F6_A0A1D5Q5F6_MACMU_9544 and tr_A0A2K6BTA1_A0A2K6BTA1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7DZF6_F7DZF6_MACMU_9544 and sp_Q5G267_NETR_MACMU_9544 are exactly identical! WARNING: Sequences tr_F7DZF6_F7DZF6_MACMU_9544 and tr_G7P658_G7P658_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7H9E1_F7H9E1_MACMU_9544 and tr_A0A2K6BN27_A0A2K6BN27_MACNE_9545 are exactly identical! WARNING: Sequences tr_B3RNP7_B3RNP7_TRIAD_10228 and tr_A0A369S8Z3_A0A369S8Z3_9METZ_287889 are exactly identical! WARNING: Sequences tr_B3SCU9_B3SCU9_TRIAD_10228 and tr_A0A369S493_A0A369S493_9METZ_287889 are exactly identical! WARNING: Sequences tr_G7PCC0_G7PCC0_MACFA_9541 and tr_A0A2K6DLA6_A0A2K6DLA6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096MQX9_A0A096MQX9_PAPAN_9555 and tr_A0A2K5KL40_A0A2K5KL40_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MV66_A0A096MV66_PAPAN_9555 and tr_A0A2K6E1M7_A0A2K6E1M7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096MV66_A0A096MV66_PAPAN_9555 and tr_A0A2K6A3M8_A0A2K6A3M8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096NZ32_A0A096NZ32_PAPAN_9555 and tr_A0A2K5NTH6_A0A2K5NTH6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NZ32_A0A096NZ32_PAPAN_9555 and tr_A0A2K5YRZ9_A0A2K5YRZ9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3LS56_A0A2I3LS56_PAPAN_9555 and tr_A0A2K5LH06_A0A2K5LH06_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3LS56_A0A2I3LS56_PAPAN_9555 and tr_A0A2K6DH39_A0A2K6DH39_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I0MGY0_A0A2I0MGY0_COLLI_8932 and tr_A0A1V4JU91_A0A1V4JU91_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1U7Q281_A0A1U7Q281_MESAU_10036 and sp_Q9WUB9_MARCO_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A226MLD1_A0A226MLD1_CALSU_9009 and tr_A0A226NQE6_A0A226NQE6_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PL46_A0A2D0PL46_ICTPU_7998 and tr_A0A2D0PL56_A0A2D0PL56_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0Q602_A0A2D0Q602_ICTPU_7998 and tr_W5U7B4_W5U7B4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QER9_A0A2D0QER9_ICTPU_7998 and tr_A0A2D0QFT7_A0A2D0QFT7_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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P21757/4_raxmlng_ancestral/P21757.raxml.reduced.phy Alignment comprises 1 partitions and 451 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 451 Gaps: 52.69 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P21757/4_raxmlng_ancestral/P21757.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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P21757/3_mltree/P21757.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 113 / 9040 [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: -178656.245713 [00:00:00 -178656.245713] Initial branch length optimization [00:00:01 -163831.740363] Model parameter optimization (eps = 0.100000) [00:00:39] Tree #1, final logLikelihood: -163421.659841 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.080682,0.306372) (0.091728,0.601672) (0.421148,0.738130) (0.406442,1.498932) 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P21757/4_raxmlng_ancestral/P21757.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P21757/4_raxmlng_ancestral/P21757.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P21757/4_raxmlng_ancestral/P21757.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P21757/4_raxmlng_ancestral/P21757.raxml.log Analysis started: 04-Jun-2021 14:17:44 / finished: 04-Jun-2021 14:18:27 Elapsed time: 42.981 seconds