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 03-Jun-2021 14:57:30 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q86YZ3/2_msa/Q86YZ3_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q86YZ3/3_mltree/Q86YZ3.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q86YZ3/4_raxmlng_ancestral/Q86YZ3 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622721450 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/Q86YZ3/2_msa/Q86YZ3_nogap_msa.fasta [00:00:00] Loaded alignment with 462 taxa and 2850 sites WARNING: Sequences tr_A0A1D5PJJ4_A0A1D5PJJ4_CHICK_9031 and tr_A0A091ILC5_A0A091ILC5_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A1D5PJJ4_A0A1D5PJJ4_CHICK_9031 and tr_A0A091VLU4_A0A091VLU4_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A1D5PJJ4_A0A1D5PJJ4_CHICK_9031 and tr_A0A087QP91_A0A087QP91_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A1D5PJJ4_A0A1D5PJJ4_CHICK_9031 and tr_A0A2I0LLS9_A0A2I0LLS9_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A1D5PJJ4_A0A1D5PJJ4_CHICK_9031 and tr_A0A1V4JZG4_A0A1V4JZG4_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1D5PJJ4_A0A1D5PJJ4_CHICK_9031 and tr_A0A226MEW3_A0A226MEW3_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A1D5PJJ4_A0A1D5PJJ4_CHICK_9031 and tr_A0A226NI21_A0A226NI21_COLVI_9014 are exactly identical! WARNING: Sequences tr_E1C251_E1C251_CHICK_9031 and tr_A0A226N1K0_A0A226N1K0_CALSU_9009 are exactly identical! WARNING: Sequences tr_E1C251_E1C251_CHICK_9031 and tr_A0A226P850_A0A226P850_COLVI_9014 are exactly identical! WARNING: Sequences tr_B9EJL3_B9EJL3_MOUSE_10090 and tr_G3H328_G3H328_CRIGR_10029 are exactly identical! WARNING: Sequences tr_B9EJL3_B9EJL3_MOUSE_10090 and tr_A0A1U7Q6F1_A0A1U7Q6F1_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3SGV1_G3SGV1_GORGO_9595 and tr_H2QP64_H2QP64_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SGV1_G3SGV1_GORGO_9595 and tr_A0A2R8ZMX9_A0A2R8ZMX9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and sp_Q6YNR6_S100B_RABIT_9986 are exactly identical! WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and tr_F6RF49_F6RF49_HORSE_9796 are exactly identical! WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and sp_P04271_S100B_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and tr_G1L2S1_G1L2S1_AILME_9646 are exactly identical! WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and tr_A0A2I2UW07_A0A2I2UW07_FELCA_9685 are exactly identical! WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and tr_A0A2Y9FKI7_A0A2Y9FKI7_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and tr_A0A384DNP5_A0A384DNP5_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2J8RC22_A0A2J8RC22_PONAB_9601 and tr_A0A383ZCB7_A0A383ZCB7_BALAS_310752 are exactly identical! WARNING: Sequences tr_H2PCU7_H2PCU7_PONAB_9601 and sp_P25815_S100P_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2PCU7_H2PCU7_PONAB_9601 and tr_F6PWQ7_F6PWQ7_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2PCU7_H2PCU7_PONAB_9601 and tr_A0A096NZC3_A0A096NZC3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2PCU7_H2PCU7_PONAB_9601 and tr_A0A0D9RU76_A0A0D9RU76_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2PCU7_H2PCU7_PONAB_9601 and tr_A0A2K5NID4_A0A2K5NID4_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2PCU7_H2PCU7_PONAB_9601 and tr_A0A2K6DNK8_A0A2K6DNK8_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2PCU7_H2PCU7_PONAB_9601 and tr_A0A2K5XH25_A0A2K5XH25_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0A0MQQ2_A0A0A0MQQ2_RABIT_9986 and sp_O77791_S10AC_RABIT_9986 are exactly identical! WARNING: Sequences tr_H2Q027_H2Q027_PANTR_9598 and tr_A0A2R9A4Q5_A0A2R9A4Q5_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5PVB6_W5PVB6_SHEEP_9940 and tr_G7PWM2_G7PWM2_MACFA_9541 are exactly identical! WARNING: Sequences tr_W5PVB6_W5PVB6_SHEEP_9940 and tr_A0A0D9R407_A0A0D9R407_CHLSB_60711 are exactly identical! WARNING: Sequences tr_W5PVB6_W5PVB6_SHEEP_9940 and tr_A0A2U3VAA5_A0A2U3VAA5_TURTR_9739 are exactly identical! WARNING: Sequences tr_W5PVB6_W5PVB6_SHEEP_9940 and tr_A0A2U3X2C1_A0A2U3X2C1_ODORO_9708 are exactly identical! WARNING: Sequences tr_W5PVB6_W5PVB6_SHEEP_9940 and tr_A0A2U3Z3M3_A0A2U3Z3M3_LEPWE_9713 are exactly identical! WARNING: Sequences tr_W5PVB6_W5PVB6_SHEEP_9940 and tr_A0A2Y9Q578_A0A2Y9Q578_DELLE_9749 are exactly identical! WARNING: Sequences tr_I3MDN4_I3MDN4_ICTTR_43179 and tr_A0A286XTU0_A0A286XTU0_CAVPO_10141 are exactly identical! WARNING: Sequences tr_B5FXV2_B5FXV2_TAEGU_59729 and tr_U3KFS2_U3KFS2_FICAL_59894 are exactly identical! WARNING: Sequences tr_H1A485_H1A485_TAEGU_59729 and tr_A0A218UDX1_A0A218UDX1_9PASE_299123 are exactly identical! WARNING: Sequences tr_U3K4U3_U3K4U3_FICAL_59894 and tr_A0A218V2N0_A0A218V2N0_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A091V497_A0A091V497_NIPNI_128390 and tr_A0A087R9H8_A0A087R9H8_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091V497_A0A091V497_NIPNI_128390 and tr_A0A091V676_A0A091V676_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091V497_A0A091V497_NIPNI_128390 and tr_A0A2I0LXI2_A0A2I0LXI2_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A2I0MMV3_A0A2I0MMV3_COLLI_8932 and tr_A0A1V4JFN9_A0A1V4JFN9_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1S3RWW0_A0A1S3RWW0_SALSA_8030 and tr_A0A060WZ60_A0A060WZ60_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A2D0QYR7_A0A2D0QYR7_ICTPU_7998 and tr_A0A2D0QYS7_A0A2D0QYS7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SZ10_A0A2D0SZ10_ICTPU_7998 and tr_A0A2D0SZ13_A0A2D0SZ13_ICTPU_7998 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/Q86YZ3/4_raxmlng_ancestral/Q86YZ3.raxml.reduced.phy Alignment comprises 1 partitions and 2850 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 2850 Gaps: 85.05 % Invariant sites: 7.51 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q86YZ3/4_raxmlng_ancestral/Q86YZ3.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/Q86YZ3/3_mltree/Q86YZ3.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 713 / 57040 [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: -282560.071910 [00:00:00 -282560.071910] Initial branch length optimization [00:00:03 -229845.180668] Model parameter optimization (eps = 0.100000) [00:02:02] Tree #1, final logLikelihood: -227648.515700 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.056155,0.565452) (0.008952,0.375675) (0.373345,0.759514) (0.561548,1.213295) 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/Q86YZ3/4_raxmlng_ancestral/Q86YZ3.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q86YZ3/4_raxmlng_ancestral/Q86YZ3.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q86YZ3/4_raxmlng_ancestral/Q86YZ3.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q86YZ3/4_raxmlng_ancestral/Q86YZ3.raxml.log Analysis started: 03-Jun-2021 14:57:30 / finished: 03-Jun-2021 14:59:45 Elapsed time: 135.464 seconds Consumed energy: 9.385 Wh