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 19-Jun-2021 19:58:12 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q05086/2_msa/Q05086_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q05086/3_mltree/Q05086.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q05086/4_raxmlng_ancestral/Q05086 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1624121892 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_040621/phylogeny-snakemake/results/Q05086/2_msa/Q05086_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 875 sites WARNING: Sequences tr_F1NBC5_F1NBC5_CHICK_9031 and tr_G1N136_G1N136_MELGA_9103 are exactly identical! WARNING: Sequences tr_A0A2I2YX52_A0A2I2YX52_GORGO_9595 and tr_A0A2I3SJZ1_A0A2I3SJZ1_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YX52_A0A2I2YX52_GORGO_9595 and sp_Q05086_UBE3A_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R445_G3R445_GORGO_9595 and tr_A0A2I3RAM0_A0A2I3RAM0_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2NAR8_H2NAR8_PONAB_9601 and tr_K7B173_K7B173_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2NAR8_H2NAR8_PONAB_9601 and tr_A0A2R9BDZ0_A0A2R9BDZ0_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A179URI7_A0A179URI7_BLAGS_559298 and tr_C5GDD8_C5GDD8_AJEDR_559297 are exactly identical! WARNING: Sequences tr_W5P440_W5P440_SHEEP_9940 and tr_E1BAV2_E1BAV2_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W5PH43_W5PH43_SHEEP_9940 and tr_A4IFN7_A4IFN7_BOVIN_9913 are exactly identical! WARNING: Sequences tr_C6HAR4_C6HAR4_AJECH_544712 and tr_F0UI26_F0UI26_AJEC8_544711 are exactly identical! WARNING: Sequences tr_A0A1D5R2K6_A0A1D5R2K6_MACMU_9544 and tr_A0A2I3MGE3_A0A2I3MGE3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5R2K6_A0A1D5R2K6_MACMU_9544 and tr_A0A2K6DXW4_A0A2K6DXW4_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FBK1_F7FBK1_MACMU_9544 and tr_G7PDD3_G7PDD3_MACFA_9541 are exactly identical! WARNING: Sequences tr_H0ZJ61_H0ZJ61_TAEGU_59729 and tr_U3JN35_U3JN35_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0ZJ61_H0ZJ61_TAEGU_59729 and tr_A0A218V507_A0A218V507_9PASE_299123 are exactly identical! WARNING: Sequences tr_G2YCG1_G2YCG1_BOTF4_999810 and tr_M7TH54_M7TH54_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2STK2_F2STK2_TRIRC_559305 and tr_A0A178EV54_A0A178EV54_TRIRU_5551 are exactly identical! WARNING: Sequences tr_U3J4R2_U3J4R2_ANAPL_8839 and tr_A0A087QJ00_A0A087QJ00_APTFO_9233 are exactly identical! WARNING: Sequences tr_U3J4R2_U3J4R2_ANAPL_8839 and tr_A0A091VDL4_A0A091VDL4_OPIHO_30419 are exactly identical! WARNING: Sequences tr_U3J4R2_U3J4R2_ANAPL_8839 and tr_A0A1V4JB33_A0A1V4JB33_PATFA_372326 are exactly identical! WARNING: Sequences tr_W2PRJ4_W2PRJ4_PHYPN_761204 and tr_W2KHV7_W2KHV7_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A096P537_A0A096P537_PAPAN_9555 and tr_A0A0D9R593_A0A0D9R593_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096P537_A0A096P537_PAPAN_9555 and tr_A0A2K5MP27_A0A2K5MP27_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096P537_A0A096P537_PAPAN_9555 and tr_A0A2K6C0X7_A0A2K6C0X7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096P537_A0A096P537_PAPAN_9555 and tr_A0A2K5YV13_A0A2K5YV13_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A151P0V4_A0A151P0V4_ALLMI_8496 and tr_A0A1U8D3T6_A0A1U8D3T6_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091VQX0_A0A091VQX0_NIPNI_128390 and tr_A0A093GK00_A0A093GK00_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A226MQF8_A0A226MQF8_CALSU_9009 and tr_A0A226P5L4_A0A226P5L4_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2K5MR62_A0A2K5MR62_CERAT_9531 and tr_A0A2K6BA20_A0A2K6BA20_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K5MR62_A0A2K5MR62_CERAT_9531 and tr_A0A2K6A2Y9_A0A2K6A2Y9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4BEW1_A0A2U4BEW1_TURTR_9739 and tr_A0A2Y9FEP9_A0A2Y9FEP9_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3ZVJ1_A0A2U3ZVJ1_ODORO_9708 and tr_A0A2Y9L642_A0A2Y9L642_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2Y9QGX9_A0A2Y9QGX9_DELLE_9749 and tr_A0A2Y9F4C9_A0A2Y9F4C9_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 33 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q05086/4_raxmlng_ancestral/Q05086.raxml.reduced.phy Alignment comprises 1 partitions and 875 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 875 Gaps: 22.56 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q05086/4_raxmlng_ancestral/Q05086.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_040621/phylogeny-snakemake/results/Q05086/3_mltree/Q05086.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 219 / 17520 [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: -386763.961588 [00:00:00 -386763.961588] Initial branch length optimization [00:00:01 -384222.668453] Model parameter optimization (eps = 0.100000) [00:00:57] Tree #1, final logLikelihood: -383255.079358 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.137037,0.317559) (0.160953,0.357940) (0.344437,0.772247) (0.357573,1.769935) 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_040621/phylogeny-snakemake/results/Q05086/4_raxmlng_ancestral/Q05086.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q05086/4_raxmlng_ancestral/Q05086.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q05086/4_raxmlng_ancestral/Q05086.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q05086/4_raxmlng_ancestral/Q05086.raxml.log Analysis started: 19-Jun-2021 19:58:12 / finished: 19-Jun-2021 19:59:17 Elapsed time: 65.762 seconds