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 02-Jun-2021 18:11:44 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q02224/2_msa/Q02224_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q02224/3_mltree/Q02224.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q02224/4_raxmlng_ancestral/Q02224 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622646704 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/Q02224/2_msa/Q02224_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 2701 sites WARNING: Sequences tr_Q5F423_Q5F423_CHICK_9031 and tr_G1N6G9_G1N6G9_MELGA_9103 are exactly identical! WARNING: Sequences tr_M3Z2F0_M3Z2F0_MUSPF_9669 and tr_E2QUS2_E2QUS2_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Z2F0_M3Z2F0_MUSPF_9669 and tr_M3X169_M3X169_FELCA_9685 are exactly identical! WARNING: Sequences tr_A0A2I3HFJ1_A0A2I3HFJ1_NOMLE_61853 and tr_G7P888_G7P888_MACFA_9541 are exactly identical! WARNING: Sequences tr_D8S915_D8S915_SELML_88036 and tr_D8SYH2_D8SYH2_SELML_88036 are exactly identical! WARNING: Sequences tr_G3QY97_G3QY97_GORGO_9595 and tr_A0A2I3RF17_A0A2I3RF17_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2QK62_H2QK62_PANTR_9598 and sp_O15066_KIF3B_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QK62_H2QK62_PANTR_9598 and tr_A0A096NUY3_A0A096NUY3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2QK62_H2QK62_PANTR_9598 and tr_A0A2K5L083_A0A2K5L083_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2QK62_H2QK62_PANTR_9598 and tr_A0A2K5Y9Z7_A0A2K5Y9Z7_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2QK62_H2QK62_PANTR_9598 and tr_A0A2R9BB24_A0A2R9BB24_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5NZV7_W5NZV7_SHEEP_9940 and tr_F1N020_F1N020_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A0E0GDI5_A0A0E0GDI5_ORYNI_4536 and tr_I1P4S5_I1P4S5_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0GDI5_A0A0E0GDI5_ORYNI_4536 and tr_A0A0D3FB40_A0A0D3FB40_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0GDI5_A0A0E0GDI5_ORYNI_4536 and tr_A0A0D9YZ41_A0A0D9YZ41_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_F6S877_F6S877_MACMU_9544 and tr_G7PGM8_G7PGM8_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6S877_F6S877_MACMU_9544 and tr_A0A2K6D218_A0A2K6D218_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7BR30_F7BR30_MACMU_9544 and tr_A0A2K6BIR9_A0A2K6BIR9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3T0G8_G3T0G8_LOXAF_9785 and tr_A0A2Y9QI24_A0A2Y9QI24_TRIMA_127582 are exactly identical! WARNING: Sequences tr_A0A0E0R9N6_A0A0E0R9N6_ORYRU_4529 and sp_Q2R2P7_KN7L_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_B3RWP1_B3RWP1_TRIAD_10228 and tr_A0A369S5D5_A0A369S5D5_9METZ_287889 are exactly identical! WARNING: Sequences tr_A0A2I2U4Q8_A0A2I2U4Q8_FELCA_9685 and tr_A0A2U3WHS7_A0A2U3WHS7_ODORO_9708 are exactly identical! WARNING: Sequences tr_M4EGD7_M4EGD7_BRARP_51351 and tr_A0A078JM02_A0A078JM02_BRANA_3708 are exactly identical! WARNING: Sequences tr_W2PPA8_W2PPA8_PHYPN_761204 and tr_A0A0W8D6C7_A0A0W8D6C7_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2PPA8_W2PPA8_PHYPN_761204 and tr_W2KCI8_W2KCI8_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2PZR3_W2PZR3_PHYPN_761204 and tr_W2KWP2_W2KWP2_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A2K6VME2_A0A2K6VME2_ONCVO_6282 and tr_A0A182EI98_A0A182EI98_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A091J8C0_A0A091J8C0_EGRGA_188379 and tr_A0A091WS06_A0A091WS06_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091J8C0_A0A091J8C0_EGRGA_188379 and tr_A0A087R2P0_A0A087R2P0_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091J8C0_A0A091J8C0_EGRGA_188379 and tr_A0A0A0B3W6_A0A0A0B3W6_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A087RF52_A0A087RF52_APTFO_9233 and tr_A0A0A0A1U0_A0A0A0A1U0_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2I0LMX4_A0A2I0LMX4_COLLI_8932 and tr_A0A1V4KKQ3_A0A1V4KKQ3_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1S4BJE8_A0A1S4BJE8_TOBAC_4097 and tr_A0A1U7WG55_A0A1U7WG55_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CK74_A0A1S4CK74_TOBAC_4097 and tr_A0A1U7V7I1_A0A1U7V7I1_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A226MHI2_A0A226MHI2_CALSU_9009 and tr_A0A226P9V5_A0A226P9V5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NJV1_A0A226NJV1_CALSU_9009 and tr_A0A226PII5_A0A226PII5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2Y9FGM5_A0A2Y9FGM5_PHYCD_9755 and tr_A0A384B241_A0A384B241_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 37 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/Q02224/4_raxmlng_ancestral/Q02224.raxml.reduced.phy Alignment comprises 1 partitions and 2701 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 2701 Gaps: 67.14 % Invariant sites: 0.78 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q02224/4_raxmlng_ancestral/Q02224.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/Q02224/3_mltree/Q02224.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 676 / 54080 [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: -631566.236048 [00:00:00 -631566.236048] Initial branch length optimization [00:00:05 -626082.688904] Model parameter optimization (eps = 0.100000) [00:03:22] Tree #1, final logLikelihood: -623702.757002 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.055715,0.111935) (0.049937,0.185286) (0.337195,0.755429) (0.557153,1.309846) 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/Q02224/4_raxmlng_ancestral/Q02224.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q02224/4_raxmlng_ancestral/Q02224.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q02224/4_raxmlng_ancestral/Q02224.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q02224/4_raxmlng_ancestral/Q02224.raxml.log Analysis started: 02-Jun-2021 18:11:44 / finished: 02-Jun-2021 18:15:33 Elapsed time: 228.579 seconds Consumed energy: 14.823 Wh