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 27-Jul-2021 09:52:37 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15354/2_msa/O15354_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15354/3_mltree/O15354.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15354/4_raxmlng_ancestral/O15354 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1627368757 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/250721_run/phylogeny-snakemake/results/O15354/2_msa/O15354_nogap_msa.fasta [00:00:00] Loaded alignment with 643 taxa and 613 sites WARNING: Sequences tr_G1S4V8_G1S4V8_NOMLE_61853 and tr_H2PD27_H2PD27_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1S4V8_G1S4V8_NOMLE_61853 and tr_A0A096NZL4_A0A096NZL4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1S8Y8_G1S8Y8_NOMLE_61853 and tr_H2Q0W6_H2Q0W6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S8Y8_G1S8Y8_NOMLE_61853 and sp_O60883_G37L1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1S8Y8_G1S8Y8_NOMLE_61853 and tr_A0A2R9BEY8_A0A2R9BEY8_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RGQ3_G3RGQ3_GORGO_9595 and tr_H2QPB3_H2QPB3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RGQ3_G3RGQ3_GORGO_9595 and tr_A0A2R8ZVR1_A0A2R8ZVR1_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8W0K6_A0A2J8W0K6_PONAB_9601 and sp_Q5IS62_NPY2R_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2J8W0K6_A0A2J8W0K6_PONAB_9601 and sp_P49146_NPY2R_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2K6HM81_A0A2K6HM81_PANTR_9598 and tr_A0A2R8ZGI9_A0A2R8ZGI9_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QVB0_H2QVB0_PANTR_9598 and sp_O15354_GPR37_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QVB0_H2QVB0_PANTR_9598 and tr_A0A2R9AID0_A0A2R9AID0_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6TEF3_F6TEF3_MACMU_9544 and tr_G8F5U1_G8F5U1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6TEF3_F6TEF3_MACMU_9544 and tr_A0A096MSR1_A0A096MSR1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6TEF3_F6TEF3_MACMU_9544 and tr_A0A0D9RNN1_A0A0D9RNN1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6TEF3_F6TEF3_MACMU_9544 and tr_A0A2K5MMR5_A0A2K5MMR5_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7AS98_F7AS98_MACMU_9544 and tr_G7P6G2_G7P6G2_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7AS98_F7AS98_MACMU_9544 and tr_A0A096NB16_A0A096NB16_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7AS98_F7AS98_MACMU_9544 and tr_A0A0D9S9S9_A0A0D9S9S9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7AS98_F7AS98_MACMU_9544 and tr_A0A2K5KH83_A0A2K5KH83_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7AS98_F7AS98_MACMU_9544 and tr_A0A2K6B674_A0A2K6B674_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7AS98_F7AS98_MACMU_9544 and tr_A0A2K5XJX6_A0A2K5XJX6_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0YRU4_H0YRU4_TAEGU_59729 and tr_A0A093S6L1_A0A093S6L1_9PASS_328815 are exactly identical! WARNING: Sequences tr_F4X6G7_F4X6G7_ACREC_103372 and tr_A0A195F227_A0A195F227_9HYME_34720 are exactly identical! WARNING: Sequences tr_G7P5D4_G7P5D4_MACFA_9541 and tr_A0A2K6D1V6_A0A2K6D1V6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I0MK11_A0A2I0MK11_COLLI_8932 and tr_A0A1V4J9G7_A0A1V4J9G7_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A226MII9_A0A226MII9_CALSU_9009 and tr_A0A226NUZ3_A0A226NUZ3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226MUC0_A0A226MUC0_CALSU_9009 and tr_A0A226P603_A0A226P603_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2K5N224_A0A2K5N224_CERAT_9531 and tr_A0A2K5Y809_A0A2K5Y809_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K6DZY9_A0A2K6DZY9_MACNE_9545 and tr_A0A2K5ZX05_A0A2K5ZX05_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4AT12_A0A2U4AT12_TURTR_9739 and tr_A0A2Y9MKV2_A0A2Y9MKV2_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 31 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15354/4_raxmlng_ancestral/O15354.raxml.reduced.phy Alignment comprises 1 partitions and 613 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 613 Gaps: 46.57 % Invariant sites: 0.16 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15354/4_raxmlng_ancestral/O15354.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/250721_run/phylogeny-snakemake/results/O15354/3_mltree/O15354.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 154 / 12320 [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: -166397.839016 [00:00:00 -166397.839016] Initial branch length optimization [00:00:01 -146171.478444] Model parameter optimization (eps = 0.100000) [00:00:50] Tree #1, final logLikelihood: -145109.861658 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.178789,0.285097) (0.129990,0.416450) (0.281575,0.569017) (0.409647,1.793431) 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/250721_run/phylogeny-snakemake/results/O15354/4_raxmlng_ancestral/O15354.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15354/4_raxmlng_ancestral/O15354.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15354/4_raxmlng_ancestral/O15354.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15354/4_raxmlng_ancestral/O15354.raxml.log Analysis started: 27-Jul-2021 09:52:37 / finished: 27-Jul-2021 09:53:31 Elapsed time: 54.106 seconds Consumed energy: 3.866 Wh