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 02:28:22 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P30566/2_msa/P30566_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P30566/3_mltree/P30566.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P30566/4_raxmlng_ancestral/P30566 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622676502 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/P30566/2_msa/P30566_nogap_msa.fasta [00:00:00] Loaded alignment with 866 taxa and 484 sites WARNING: Sequences tr_J3KD00_J3KD00_COCIM_246410 and tr_A0A0J6YMS2_A0A0J6YMS2_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QK48_B6QK48_TALMQ_441960 and tr_A0A093XNY4_A0A093XNY4_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2VWL9_B2VWL9_PYRTR_426418 and tr_A0A2W1ERP6_A0A2W1ERP6_9PLEO_45151 are exactly identical! WARNING: Sequences tr_B8NGE1_B8NGE1_ASPFN_332952 and tr_Q2UEW5_Q2UEW5_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8NGE1_B8NGE1_ASPFN_332952 and tr_A0A0F0I3G5_A0A0F0I3G5_ASPPU_1403190 are exactly identical! WARNING: Sequences tr_B8NGE1_B8NGE1_ASPFN_332952 and tr_A0A1S9E0I3_A0A1S9E0I3_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A2I3TVQ6_A0A2I3TVQ6_PANTR_9598 and tr_A0A2R9A5Q2_A0A2R9A5Q2_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9FFI2_F9FFI2_FUSOF_660025 and tr_A0A2H3TNF3_A0A2H3TNF3_FUSOX_5507 are exactly identical! WARNING: Sequences tr_A2QCL8_A2QCL8_ASPNC_425011 and tr_G3Y2L0_G3Y2L0_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QCL8_A2QCL8_ASPNC_425011 and tr_A0A319B889_A0A319B889_9EURO_1450533 are exactly identical! WARNING: Sequences tr_F4P2T3_F4P2T3_BATDJ_684364 and tr_A0A177WMM7_A0A177WMM7_BATDE_403673 are exactly identical! WARNING: Sequences tr_F9X6V2_F9X6V2_ZYMTI_336722 and tr_A0A1X7RMS1_A0A1X7RMS1_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2Y2W4_G2Y2W4_BOTF4_999810 and tr_M7UPD7_M7UPD7_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2SSE0_F2SSE0_TRIRC_559305 and tr_A0A178EUQ2_A0A178EUQ2_TRIRU_5551 are exactly identical! WARNING: Sequences tr_A0A0C4DI49_A0A0C4DI49_FUSO4_426428 and tr_N4UTI4_N4UTI4_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_A0A0C4DI49_A0A0C4DI49_FUSO4_426428 and tr_X0BGJ6_X0BGJ6_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_A0A0C4DI49_A0A0C4DI49_FUSO4_426428 and tr_A0A2H3G871_A0A2H3G871_FUSOX_327505 are exactly identical! WARNING: Sequences tr_F2Q0A0_F2Q0A0_TRIEC_559882 and tr_A0A059JD97_A0A059JD97_9EURO_1215338 are exactly identical! WARNING: Sequences tr_S0EPH4_S0EPH4_GIBF5_1279085 and tr_A0A365NNT6_A0A365NNT6_GIBIN_948311 are exactly identical! WARNING: Sequences tr_U5H511_U5H511_USTV1_683840 and tr_A0A2X0P669_A0A2X0P669_9BASI_796604 are exactly identical! WARNING: Sequences tr_W2RB71_W2RB71_PHYPN_761204 and tr_A0A0W8DKP5_A0A0W8DKP5_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2RB71_W2RB71_PHYPN_761204 and tr_W2H3J0_W2H3J0_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A015KQG0_A0A015KQG0_9GLOM_1432141 and tr_A0A2H5R3V9_A0A2H5R3V9_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A2I3MBW4_A0A2I3MBW4_PAPAN_9555 and tr_A0A2K5N6Y9_A0A2K5N6Y9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A094DZG4_A0A094DZG4_9PEZI_1420912 and tr_A0A1B8GJL0_A0A1B8GJL0_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0F9XAV3_A0A0F9XAV3_TRIHA_5544 and tr_A0A2T3ZXI8_A0A2T3ZXI8_TRIHA_983964 are exactly identical! WARNING: Sequences tr_A0A0A1N300_A0A0A1N300_9FUNG_58291 and tr_A0A367JHN8_A0A367JHN8_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0G4P5N6_A0A0G4P5N6_PENCA_1429867 and tr_A0A1V6QVG1_A0A1V6QVG1_9EURO_60172 are exactly identical! WARNING: Sequences tr_A0A0V0SK41_A0A0V0SK41_9BILA_6336 and tr_A0A0V1CEE4_A0A0V1CEE4_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0SK41_A0A0V0SK41_9BILA_6336 and tr_A0A0V0ZT16_A0A0V0ZT16_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0SK41_A0A0V0SK41_9BILA_6336 and tr_A0A0V1PG90_A0A0V1PG90_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0SK41_A0A0V0SK41_9BILA_6336 and tr_A0A0V0UDH2_A0A0V0UDH2_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A100I4Y0_A0A100I4Y0_ASPNG_5061 and tr_A0A1L9NAI2_A0A1L9NAI2_ASPTU_767770 are exactly identical! WARNING: Sequences tr_A0A100I4Y0_A0A100I4Y0_ASPNG_5061 and tr_A0A317VFD9_A0A317VFD9_9EURO_1448314 are exactly identical! WARNING: Sequences tr_A0A226MGP7_A0A226MGP7_CALSU_9009 and tr_A0A226NWN4_A0A226NWN4_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2H3BTX4_A0A2H3BTX4_9AGAR_1076256 and tr_A0A284QYH5_A0A284QYH5_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2G5HP02_A0A2G5HP02_CERBT_122368 and tr_A0A2S6C022_A0A2S6C022_9PEZI_357750 are exactly identical! WARNING: Sequences tr_A0A2N5S2R3_A0A2N5S2R3_9BASI_200324 and tr_A0A2N5S2U6_A0A2N5S2U6_9BASI_200324 are exactly identical! WARNING: Sequences tr_A0A2S7NT39_A0A2S7NT39_9HELO_2070414 and tr_A0A2S7QP72_A0A2S7QP72_9HELO_2070412 are exactly identical! WARNING: Sequences tr_A0A2V5ICA6_A0A2V5ICA6_9EURO_1450541 and tr_A0A2V5GYF2_A0A2V5GYF2_9EURO_1450538 are exactly identical! WARNING: Duplicate sequences found: 40 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/P30566/4_raxmlng_ancestral/P30566.raxml.reduced.phy Alignment comprises 1 partitions and 484 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 484 Gaps: 7.72 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P30566/4_raxmlng_ancestral/P30566.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/P30566/3_mltree/P30566.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 121 / 9680 [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: -154102.686526 [00:00:00 -154102.686526] Initial branch length optimization [00:00:00 -153603.241134] Model parameter optimization (eps = 0.100000) [00:00:38] Tree #1, final logLikelihood: -153005.674943 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.258785,0.337917) (0.333803,0.504364) (0.245924,1.018865) (0.161487,3.056775) 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/P30566/4_raxmlng_ancestral/P30566.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P30566/4_raxmlng_ancestral/P30566.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P30566/4_raxmlng_ancestral/P30566.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P30566/4_raxmlng_ancestral/P30566.raxml.log Analysis started: 03-Jun-2021 02:28:22 / finished: 03-Jun-2021 02:29:04 Elapsed time: 42.092 seconds Consumed energy: 3.449 Wh