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 02:15:58 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P05067/2_msa/P05067_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P05067/3_mltree/P05067.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P05067/4_raxmlng_ancestral/P05067 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622675758 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/P05067/2_msa/P05067_nogap_msa.fasta [00:00:00] Loaded alignment with 989 taxa and 770 sites WARNING: Sequences tr_A0A2I2Z327_A0A2I2Z327_GORGO_9595 and tr_A0A2R9AFK0_A0A2R9AFK0_PANPA_9597 are exactly identical! WARNING: Sequences tr_A7SCV3_A7SCV3_NEMVE_45351 and tr_A7TCY8_A7TCY8_NEMVE_45351 are exactly identical! WARNING: Sequences tr_G2HDV8_G2HDV8_PANTR_9598 and tr_A0A2R9AND8_A0A2R9AND8_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7ALK1_K7ALK1_PANTR_9598 and tr_A0A2R9BZB3_A0A2R9BZB3_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q5IS80_A4_PANTR_9598 and tr_A0A2R8ZFM4_A0A2R8ZFM4_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5Q110_A0A1D5Q110_MACMU_9544 and tr_A0A096MXA8_A0A096MXA8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5Q110_A0A1D5Q110_MACMU_9544 and tr_A0A0D9S4Q6_A0A0D9S4Q6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5Q110_A0A1D5Q110_MACMU_9544 and tr_A0A2K5N9J6_A0A2K5N9J6_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7MNB1_G7MNB1_MACMU_9544 and tr_A0A0D9R9L3_A0A0D9R9L3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7MNB1_G7MNB1_MACMU_9544 and tr_A0A2K5NQN0_A0A2K5NQN0_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7MNB1_G7MNB1_MACMU_9544 and tr_A0A2K6ECD1_A0A2K6ECD1_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7N4Q1_G7N4Q1_MACMU_9544 and tr_A0A096NX59_A0A096NX59_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7N4Q1_G7N4Q1_MACMU_9544 and tr_A0A2K5NUH3_A0A2K5NUH3_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7N4Q1_G7N4Q1_MACMU_9544 and tr_A0A2K6D4C6_A0A2K6D4C6_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7N4Q1_G7N4Q1_MACMU_9544 and tr_A0A2K5YFF9_A0A2K5YFF9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A044TIP2_A0A044TIP2_ONCVO_6282 and tr_A0A182DXZ4_A0A182DXZ4_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A096NX55_A0A096NX55_PAPAN_9555 and tr_A0A0D9RPK9_A0A0D9RPK9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A0A0MUB4_A0A0A0MUB4_PAPAN_9555 and tr_A0A0D9QVT2_A0A0D9QVT2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A0A0MUB4_A0A0A0MUB4_PAPAN_9555 and tr_A0A2K6B6R5_A0A2K6B6R5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0A0MUB4_A0A0A0MUB4_PAPAN_9555 and tr_A0A2K5YWS0_A0A2K5YWS0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0D9QWA5_A0A0D9QWA5_CHLSB_60711 and tr_A0A2K5L5F3_A0A2K5L5F3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0V1D6I8_A0A0V1D6I8_TRIBR_45882 and tr_A0A0V0VBR3_A0A0V0VBR3_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1D6I8_A0A0V1D6I8_TRIBR_45882 and tr_A0A0V0UE62_A0A0V0UE62_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1D6J9_A0A0V1D6J9_TRIBR_45882 and tr_A0A0V1LSE5_A0A0V1LSE5_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0WNE2_A0A0V0WNE2_9BILA_92179 and tr_A0A0V1LC71_A0A0V1LC71_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0WNE2_A0A0V0WNE2_9BILA_92179 and tr_A0A0V1P2B6_A0A0V1P2B6_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A1S3D2P3_A0A1S3D2P3_DIACI_121845 and tr_A0A1S4EC39_A0A1S4EC39_DIACI_121845 are exactly identical! WARNING: Sequences tr_A0A2D0SVS2_A0A2D0SVS2_ICTPU_7998 and tr_A0A2D0SVT4_A0A2D0SVT4_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/020621_run/phylogeny-snakemake/results/P05067/4_raxmlng_ancestral/P05067.raxml.reduced.phy Alignment comprises 1 partitions and 770 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 770 Gaps: 63.21 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P05067/4_raxmlng_ancestral/P05067.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/P05067/3_mltree/P05067.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 193 / 15440 [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: -218895.558375 [00:00:00 -218895.558375] Initial branch length optimization [00:00:02 -205247.575652] Model parameter optimization (eps = 0.100000) [00:00:57] Tree #1, final logLikelihood: -204497.100217 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.050272,0.186523) (0.048138,0.383889) (0.398875,0.770121) (0.502716,1.322739) 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/P05067/4_raxmlng_ancestral/P05067.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P05067/4_raxmlng_ancestral/P05067.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P05067/4_raxmlng_ancestral/P05067.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P05067/4_raxmlng_ancestral/P05067.raxml.log Analysis started: 03-Jun-2021 02:15:58 / finished: 03-Jun-2021 02:17:03 Elapsed time: 64.961 seconds Consumed energy: 5.234 Wh