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 14:22:06 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P14780/2_msa/P14780_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P14780/3_mltree/P14780.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P14780/4_raxmlng_ancestral/P14780 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622805726 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/P14780/2_msa/P14780_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 707 sites WARNING: Sequences tr_G1T8Z9_G1T8Z9_RABIT_9986 and sp_P28863_MMP3_RABIT_9986 are exactly identical! WARNING: Sequences tr_A0A2I3TEQ9_A0A2I3TEQ9_PANTR_9598 and sp_P08253_MMP2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3TEQ9_A0A2I3TEQ9_PANTR_9598 and tr_A0A096NIF0_A0A096NIF0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3TEQ9_A0A2I3TEQ9_PANTR_9598 and tr_A0A0D9QZ11_A0A0D9QZ11_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3TEQ9_A0A2I3TEQ9_PANTR_9598 and tr_A0A2K5KTG2_A0A2K5KTG2_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3TEQ9_A0A2I3TEQ9_PANTR_9598 and tr_A0A2K6BWB4_A0A2K6BWB4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3TEQ9_A0A2I3TEQ9_PANTR_9598 and tr_A0A2K5ZKS9_A0A2K5ZKS9_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2Q4N2_H2Q4N2_PANTR_9598 and tr_A0A2R9BCT7_A0A2R9BCT7_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6T9W9_F6T9W9_HORSE_9796 and sp_Q28397_MMP3_HORSE_9796 are exactly identical! WARNING: Sequences tr_A0A1D5QFN4_A0A1D5QFN4_MACMU_9544 and tr_G7PNK8_G7PNK8_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6YVM2_F6YVM2_MACMU_9544 and tr_G7PNK7_G7PNK7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7FE85_F7FE85_MACMU_9544 and tr_G7PNJ9_G7PNJ9_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7FE85_F7FE85_MACMU_9544 and tr_A0A096N6P6_A0A096N6P6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7FE85_F7FE85_MACMU_9544 and tr_A0A0D9S1T7_A0A0D9S1T7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7FE85_F7FE85_MACMU_9544 and tr_A0A2K5P0Y0_A0A2K5P0Y0_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7FE85_F7FE85_MACMU_9544 and tr_A0A2K5YEA4_A0A2K5YEA4_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7GQW5_F7GQW5_MACMU_9544 and tr_G7PNK1_G7PNK1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GQW6_F7GQW6_MACMU_9544 and tr_A0A2K6AZ02_A0A2K6AZ02_MACNE_9545 are exactly identical! WARNING: Sequences tr_F1MF56_F1MF56_BOVIN_9913 and sp_P52176_MMP9_BOVIN_9913 are exactly identical! WARNING: Sequences tr_G5E5A9_G5E5A9_BOVIN_9913 and sp_P07589_FINC_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A096NXU1_A0A096NXU1_PAPAN_9555 and tr_A0A2K5NYX0_A0A2K5NYX0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NXU1_A0A096NXU1_PAPAN_9555 and tr_A0A2K5YCD5_A0A2K5YCD5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3MI87_A0A2I3MI87_PAPAN_9555 and tr_A0A2K5YGD1_A0A2K5YGD1_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A226N9V4_A0A226N9V4_CALSU_9009 and tr_A0A226P7U0_A0A226P7U0_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0Q1X9_A0A2D0Q1X9_ICTPU_7998 and tr_A0A2D0Q359_A0A2D0Q359_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0Q1X9_A0A2D0Q1X9_ICTPU_7998 and tr_A0A2D0Q4W7_A0A2D0Q4W7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5ME47_A0A2K5ME47_CERAT_9531 and tr_A0A2K6AA62_A0A2K6AA62_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5P0B7_A0A2K5P0B7_CERAT_9531 and tr_A0A2K6A3K3_A0A2K6A3K3_MANLE_9568 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/P14780/4_raxmlng_ancestral/P14780.raxml.reduced.phy Alignment comprises 1 partitions and 707 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 707 Gaps: 33.89 % Invariant sites: 0.28 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P14780/4_raxmlng_ancestral/P14780.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/P14780/3_mltree/P14780.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 177 / 14160 [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: -227107.364204 [00:00:00 -227107.364204] Initial branch length optimization [00:00:03 -226457.520556] Model parameter optimization (eps = 0.100000) [00:03:00] Tree #1, final logLikelihood: -225559.621758 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.149258,0.332156) (0.180744,0.470718) (0.346783,0.945396) (0.323215,1.662970) 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/P14780/4_raxmlng_ancestral/P14780.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P14780/4_raxmlng_ancestral/P14780.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P14780/4_raxmlng_ancestral/P14780.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/P14780/4_raxmlng_ancestral/P14780.raxml.log Analysis started: 04-Jun-2021 14:22:06 / finished: 04-Jun-2021 14:25:14 Elapsed time: 187.221 seconds