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 12-Jul-2021 17:21:26 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O75800/2_msa/O75800_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O75800/3_mltree/O75800.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O75800/4_raxmlng_ancestral/O75800 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626099686 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/300621_run/phylogeny-snakemake/results/O75800/2_msa/O75800_nogap_msa.fasta [00:00:00] Loaded alignment with 772 taxa and 440 sites WARNING: Sequences tr_E3RG26_E3RG26_PYRTT_861557 and tr_E3S4E6_E3S4E6_PYRTT_861557 are exactly identical! WARNING: Sequences tr_G3SCV8_G3SCV8_GORGO_9595 and tr_H2N3E5_H2N3E5_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3SCV8_G3SCV8_GORGO_9595 and tr_K7C5B9_K7C5B9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SCV8_G3SCV8_GORGO_9595 and sp_Q9GZT9_EGLN1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3SCV8_G3SCV8_GORGO_9595 and tr_F7BR59_F7BR59_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3SCV8_G3SCV8_GORGO_9595 and tr_F6TN62_F6TN62_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3SCV8_G3SCV8_GORGO_9595 and tr_A0A096NFY5_A0A096NFY5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3SCV8_G3SCV8_GORGO_9595 and tr_A0A0D9RD30_A0A0D9RD30_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3SCV8_G3SCV8_GORGO_9595 and tr_A0A2K5NNC9_A0A2K5NNC9_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3SCV8_G3SCV8_GORGO_9595 and tr_A0A2K6DHY0_A0A2K6DHY0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A179V4I4_A0A179V4I4_BLAGS_559298 and tr_A0A179U8A0_A0A179U8A0_AJEDR_559297 are exactly identical! WARNING: Sequences tr_F9G167_F9G167_FUSOF_660025 and tr_A0A0D2XI31_A0A0D2XI31_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9G167_F9G167_FUSOF_660025 and tr_N4U7C7_N4U7C7_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9G167_F9G167_FUSOF_660025 and tr_X0CVP8_X0CVP8_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9G167_F9G167_FUSOF_660025 and tr_A0A2H3TEL2_A0A2H3TEL2_FUSOX_5507 are exactly identical! WARNING: Sequences tr_A0A0B2XHW9_A0A0B2XHW9_METRA_655844 and tr_A0A0D9P8V9_A0A0D9P8V9_METAN_1291518 are exactly identical! WARNING: Sequences tr_E9F3N9_E9F3N9_METRA_655844 and tr_A0A0D9NVN0_A0A0D9NVN0_METAN_1291518 are exactly identical! WARNING: Sequences tr_M3WV78_M3WV78_FELCA_9685 and tr_A0A2U3UYG0_A0A2U3UYG0_TURTR_9739 are exactly identical! WARNING: Sequences tr_M3WV78_M3WV78_FELCA_9685 and tr_A0A2U3W9F4_A0A2U3W9F4_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3WV78_M3WV78_FELCA_9685 and tr_A0A2Y9L6Z4_A0A2Y9L6Z4_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3WV78_M3WV78_FELCA_9685 and tr_A0A2Y9LHE3_A0A2Y9LHE3_DELLE_9749 are exactly identical! WARNING: Sequences tr_M3WV78_M3WV78_FELCA_9685 and tr_A0A2Y9FNN4_A0A2Y9FNN4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_V2X0R0_V2X0R0_MONRO_1381753 and tr_A0A0W0F557_A0A0W0F557_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2Q1P9_W2Q1P9_PHYPN_761204 and tr_W2KZ45_W2KZ45_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A3B6NPX8_A0A3B6NPX8_WHEAT_4565 and tr_A0A3B6PNB1_A0A3B6PNB1_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A3B6NPX8_A0A3B6NPX8_WHEAT_4565 and tr_A0A3B6QGX2_A0A3B6QGX2_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A015JNI5_A0A015JNI5_9GLOM_1432141 and tr_A0A2H5S9L7_A0A2H5S9L7_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015KPV6_A0A015KPV6_9GLOM_1432141 and tr_A0A2H5SL73_A0A2H5SL73_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015L412_A0A015L412_9GLOM_1432141 and tr_A0A2H5TC01_A0A2H5TC01_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A015M8K3_A0A015M8K3_9GLOM_1432141 and tr_A0A2H5RK43_A0A2H5RK43_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A096NDA6_A0A096NDA6_PAPAN_9555 and tr_A0A2K5KIB8_A0A2K5KIB8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NDA6_A0A096NDA6_PAPAN_9555 and tr_A0A2K6DKS8_A0A2K6DKS8_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A067CCM8_A0A067CCM8_SAPPC_695850 and tr_T0S6J2_T0S6J2_9STRA_1156394 are exactly identical! WARNING: Sequences tr_A0A1D1US41_A0A1D1US41_RAMVA_947166 and tr_A0A1D1V241_A0A1D1V241_RAMVA_947166 are exactly identical! WARNING: Sequences tr_A0A2H3AHQ9_A0A2H3AHQ9_9AGAR_1076256 and tr_A0A2H3ALM2_A0A2H3ALM2_9AGAR_1076256 are exactly identical! WARNING: Duplicate sequences found: 35 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O75800/4_raxmlng_ancestral/O75800.raxml.reduced.phy Alignment comprises 1 partitions and 440 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 440 Gaps: 57.77 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O75800/4_raxmlng_ancestral/O75800.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/300621_run/phylogeny-snakemake/results/O75800/3_mltree/O75800.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 110 / 8800 [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: -209941.083472 [00:00:00 -209941.083472] Initial branch length optimization [00:00:01 -179908.853400] Model parameter optimization (eps = 0.100000) [00:00:57] Tree #1, final logLikelihood: -179423.796702 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.050278,0.169826) (0.119904,0.601448) (0.502782,0.846669) (0.327036,1.509484) 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/300621_run/phylogeny-snakemake/results/O75800/4_raxmlng_ancestral/O75800.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O75800/4_raxmlng_ancestral/O75800.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O75800/4_raxmlng_ancestral/O75800.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O75800/4_raxmlng_ancestral/O75800.raxml.log Analysis started: 12-Jul-2021 17:21:26 / finished: 12-Jul-2021 17:22:27 Elapsed time: 60.918 seconds Consumed energy: 5.626 Wh