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 02:44:26 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P54760/2_msa/P54760_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P54760/3_mltree/P54760.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P54760/4_raxmlng_ancestral/P54760 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622677466 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/P54760/2_msa/P54760_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 987 sites WARNING: Sequences tr_A0A1I7Q3Z3_A0A1I7Q3Z3_CHICK_9031 and sp_Q07496_EPHA4_CHICK_9031 are exactly identical! WARNING: Sequences tr_F1NHC7_F1NHC7_CHICK_9031 and sp_P28693_EPHB2_CHICK_9031 are exactly identical! WARNING: Sequences tr_A0A2I2YR65_A0A2I2YR65_GORGO_9595 and sp_P54753_EPHB3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QUG2_G3QUG2_GORGO_9595 and tr_G1SDT6_G1SDT6_RABIT_9986 are exactly identical! WARNING: Sequences tr_G3QUG2_G3QUG2_GORGO_9595 and tr_H2QTF1_H2QTF1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QUG2_G3QUG2_GORGO_9595 and sp_Q15375_EPHA7_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QUG2_G3QUG2_GORGO_9595 and tr_G7MPY1_G7MPY1_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QUG2_G3QUG2_GORGO_9595 and tr_F6XPG2_F6XPG2_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3QUG2_G3QUG2_GORGO_9595 and tr_G7P422_G7P422_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3QUG2_G3QUG2_GORGO_9595 and tr_A0A096NGE6_A0A096NGE6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3QUG2_G3QUG2_GORGO_9595 and tr_A0A2K5KXK5_A0A2K5KXK5_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3QUG2_G3QUG2_GORGO_9595 and tr_A0A2K6CFV5_A0A2K6CFV5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3QUG2_G3QUG2_GORGO_9595 and tr_A0A2K6ACW3_A0A2K6ACW3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2J8NFU1_A0A2J8NFU1_PANTR_9598 and sp_P54764_EPHA4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8NFU1_A0A2J8NFU1_PANTR_9598 and tr_G7N911_G7N911_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2J8NFU1_A0A2J8NFU1_PANTR_9598 and tr_G7PK59_G7PK59_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2J8NFU1_A0A2J8NFU1_PANTR_9598 and tr_A0A096MZK5_A0A096MZK5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2J8NFU1_A0A2J8NFU1_PANTR_9598 and tr_A0A0D9R686_A0A0D9R686_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2J8NFU1_A0A2J8NFU1_PANTR_9598 and tr_A0A2K5MZS6_A0A2K5MZS6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2J8NFU1_A0A2J8NFU1_PANTR_9598 and tr_A0A2R9CME8_A0A2R9CME8_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QV43_H2QV43_PANTR_9598 and sp_P54760_EPHB4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2RC21_H2RC21_PANTR_9598 and tr_A0A2R8ZM22_A0A2R8ZM22_PANPA_9597 are exactly identical! WARNING: Sequences tr_M4A1M4_M4A1M4_XIPMA_8083 and tr_A0A087Y9M1_A0A087Y9M1_POEFO_48698 are exactly identical! WARNING: Sequences tr_F7DM14_F7DM14_MACMU_9544 and tr_G7NXX9_G7NXX9_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7DM14_F7DM14_MACMU_9544 and tr_A0A096MU83_A0A096MU83_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7DM14_F7DM14_MACMU_9544 and tr_A0A0D9REN6_A0A0D9REN6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7DM14_F7DM14_MACMU_9544 and tr_A0A2K5KKM8_A0A2K5KKM8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7DM14_F7DM14_MACMU_9544 and tr_A0A2K6EB70_A0A2K6EB70_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7EGZ3_F7EGZ3_MACMU_9544 and tr_A0A2K5KUL3_A0A2K5KUL3_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7HDY6_F7HDY6_MACMU_9544 and tr_A0A2K6CN86_A0A2K6CN86_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0ZQ33_H0ZQ33_TAEGU_59729 and tr_A0A093QGM2_A0A093QGM2_9PASS_328815 are exactly identical! WARNING: Sequences tr_G7P5R2_G7P5R2_MACFA_9541 and tr_A0A2K5MGB6_A0A2K5MGB6_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7P5R2_G7P5R2_MACFA_9541 and tr_A0A2K6AUI6_A0A2K6AUI6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096NWC8_A0A096NWC8_PAPAN_9555 and tr_A0A2K5MME4_A0A2K5MME4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A091W3D8_A0A091W3D8_NIPNI_128390 and tr_A0A087R738_A0A087R738_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A2D0QAC9_A0A2D0QAC9_ICTPU_7998 and tr_A0A2D0QBH4_A0A2D0QBH4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QAC9_A0A2D0QAC9_ICTPU_7998 and tr_A0A2D0QE47_A0A2D0QE47_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QAC9_A0A2D0QAC9_ICTPU_7998 and tr_A0A2D0QE52_A0A2D0QE52_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QBH6_A0A2D0QBH6_ICTPU_7998 and tr_A0A2D0QD49_A0A2D0QD49_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RDR8_A0A2D0RDR8_ICTPU_7998 and tr_A0A2D0RDS7_A0A2D0RDS7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0REW8_A0A2D0REW8_ICTPU_7998 and tr_A0A2D0RFK9_A0A2D0RFK9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T8T2_A0A2D0T8T2_ICTPU_7998 and tr_W6A394_W6A394_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5N4K5_A0A2K5N4K5_CERAT_9531 and tr_A0A2K6DPE2_A0A2K6DPE2_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K5N4K5_A0A2K5N4K5_CERAT_9531 and tr_A0A2K6AKF8_A0A2K6AKF8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4ADT2_A0A2U4ADT2_TURTR_9739 and tr_A0A2Y9N2K4_A0A2Y9N2K4_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4AVL5_A0A2U4AVL5_TURTR_9739 and tr_A0A2Y9LT25_A0A2Y9LT25_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3WZC6_A0A2U3WZC6_ODORO_9708 and tr_A0A2Y9KS10_A0A2Y9KS10_ENHLU_391180 are exactly identical! WARNING: Duplicate sequences found: 47 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/P54760/4_raxmlng_ancestral/P54760.raxml.reduced.phy Alignment comprises 1 partitions and 987 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 987 Gaps: 6.89 % Invariant sites: 1.52 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P54760/4_raxmlng_ancestral/P54760.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/P54760/3_mltree/P54760.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 247 / 19760 [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: -194268.833699 [00:00:00 -194268.833699] Initial branch length optimization [00:00:01 -194091.467995] Model parameter optimization (eps = 0.100000) [00:00:37] Tree #1, final logLikelihood: -193611.135904 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.272272,0.347738) (0.233821,0.599101) (0.308917,1.016985) (0.184991,2.438364) 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/P54760/4_raxmlng_ancestral/P54760.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P54760/4_raxmlng_ancestral/P54760.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P54760/4_raxmlng_ancestral/P54760.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P54760/4_raxmlng_ancestral/P54760.raxml.log Analysis started: 03-Jun-2021 02:44:26 / finished: 03-Jun-2021 02:45:11 Elapsed time: 45.414 seconds Consumed energy: 3.172 Wh