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 03-Jun-2021 02:49:41 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P13645/2_msa/P13645_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P13645/3_mltree/P13645.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P13645/4_raxmlng_ancestral/P13645 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622677781 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/P13645/2_msa/P13645_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 584 sites WARNING: Sequences tr_A0A1D5PZ89_A0A1D5PZ89_CHICK_9031 and sp_Q6PVZ1_K1C14_CHICK_9031 are exactly identical! WARNING: Sequences tr_G3RL08_G3RL08_GORGO_9595 and sp_A5A6M5_K1H1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RL08_G3RL08_GORGO_9595 and sp_Q15323_K1H1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RL08_G3RL08_GORGO_9595 and tr_A0A2R9CQW6_A0A2R9CQW6_PANPA_9597 are exactly identical! WARNING: Sequences sp_A5A6N2_K1C25_PANTR_9598 and tr_H2QCW9_H2QCW9_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2QCC4_H2QCC4_PANTR_9598 and tr_A0A2R9BI07_A0A2R9BI07_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QCX1_H2QCX1_PANTR_9598 and tr_A0A2R9BZA1_A0A2R9BZA1_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QCZ2_H2QCZ2_PANTR_9598 and tr_A0A2R9ATZ6_A0A2R9ATZ6_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QCZ4_H2QCZ4_PANTR_9598 and tr_A0A2R8ZHV6_A0A2R8ZHV6_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QCZ8_H2QCZ8_PANTR_9598 and tr_A0A2R9BML2_A0A2R9BML2_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R114_H2R114_PANTR_9598 and tr_A0A2R9ALU5_A0A2R9ALU5_PANPA_9597 are exactly identical! WARNING: Sequences sp_B0LKP1_KRT35_SHEEP_9940 and tr_W5Q5N5_W5Q5N5_SHEEP_9940 are exactly identical! WARNING: Sequences tr_A0A1D5Q3N1_A0A1D5Q3N1_MACMU_9544 and tr_G7PUS3_G7PUS3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7A635_F7A635_MACMU_9544 and tr_A0A2I3MA29_A0A2I3MA29_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7A635_F7A635_MACMU_9544 and tr_A0A0D9S2G2_A0A0D9S2G2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7A670_F7A670_MACMU_9544 and tr_G7PUS4_G7PUS4_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7B5C2_F7B5C2_MACMU_9544 and tr_G7PUQ0_G7PUQ0_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7B5C2_F7B5C2_MACMU_9544 and tr_A0A2K6AP56_A0A2K6AP56_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7B5I4_F7B5I4_MACMU_9544 and tr_A0A2K6EC66_A0A2K6EC66_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7B5M7_F7B5M7_MACMU_9544 and tr_A0A2K5KWM8_A0A2K5KWM8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7B5M7_F7B5M7_MACMU_9544 and tr_A0A2K6BB16_A0A2K6BB16_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7B5M7_F7B5M7_MACMU_9544 and tr_A0A2K6AF67_A0A2K6AF67_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7FXZ9_F7FXZ9_MACMU_9544 and tr_G7PUR5_G7PUR5_MACFA_9541 are exactly identical! WARNING: Sequences tr_B0BMI8_B0BMI8_XENTR_8364 and tr_F6RGW5_F6RGW5_XENTR_8364 are exactly identical! WARNING: Sequences tr_A0A096P5J0_A0A096P5J0_PAPAN_9555 and tr_A0A0D9S2W8_A0A0D9S2W8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3MX15_A0A2I3MX15_PAPAN_9555 and tr_A0A2K5KRV7_A0A2K5KRV7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MX15_A0A2I3MX15_PAPAN_9555 and tr_A0A2K6A821_A0A2K6A821_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A091UUY7_A0A091UUY7_NIPNI_128390 and tr_A0A091GDA1_A0A091GDA1_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091VY56_A0A091VY56_NIPNI_128390 and tr_A0A0A0APW4_A0A0A0APW4_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2K5P1B1_A0A2K5P1B1_CERAT_9531 and tr_A0A2K5ZJV4_A0A2K5ZJV4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5P1P6_A0A2K5P1P6_CERAT_9531 and tr_A0A2K5Y3D0_A0A2K5Y3D0_MANLE_9568 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/020621_run/phylogeny-snakemake/results/P13645/4_raxmlng_ancestral/P13645.raxml.reduced.phy Alignment comprises 1 partitions and 584 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 584 Gaps: 32.07 % Invariant sites: 2.40 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P13645/4_raxmlng_ancestral/P13645.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/P13645/3_mltree/P13645.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 146 / 11680 [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: -139719.370447 [00:00:00 -139719.370447] Initial branch length optimization [00:00:01 -135481.074205] Model parameter optimization (eps = 0.100000) [00:00:27] Tree #1, final logLikelihood: -134987.186376 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.191588,0.321495) (0.136753,0.623243) (0.383330,0.913470) (0.288329,1.744585) 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/P13645/4_raxmlng_ancestral/P13645.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P13645/4_raxmlng_ancestral/P13645.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P13645/4_raxmlng_ancestral/P13645.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P13645/4_raxmlng_ancestral/P13645.raxml.log Analysis started: 03-Jun-2021 02:49:41 / finished: 03-Jun-2021 02:50:13 Elapsed time: 32.098 seconds Consumed energy: 2.355 Wh