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 18:36:11 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9H3H5/2_msa/Q9H3H5_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9H3H5/3_mltree/Q9H3H5.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9H3H5/4_raxmlng_ancestral/Q9H3H5 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622648171 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/Q9H3H5/2_msa/Q9H3H5_nogap_msa.fasta [00:00:00] Loaded alignment with 986 taxa and 408 sites WARNING: Sequences tr_G3QYF6_G3QYF6_GORGO_9595 and tr_H2R3F6_H2R3F6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QYF6_G3QYF6_GORGO_9595 and tr_A0A2R9C1T0_A0A2R9C1T0_PANPA_9597 are exactly identical! WARNING: Sequences tr_C0NNE1_C0NNE1_AJECG_447093 and tr_C6H330_C6H330_AJECH_544712 are exactly identical! WARNING: Sequences tr_C0NNE1_C0NNE1_AJECG_447093 and tr_F0U6E4_F0U6E4_AJEC8_544711 are exactly identical! WARNING: Sequences tr_A0A179U7Z0_A0A179U7Z0_BLAGS_559298 and tr_C5GPC5_C5GPC5_AJEDR_559297 are exactly identical! WARNING: Sequences tr_F9FI32_F9FI32_FUSOF_660025 and tr_N4UYM8_N4UYM8_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FI32_F9FI32_FUSOF_660025 and tr_X0CSJ1_X0CSJ1_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FI32_F9FI32_FUSOF_660025 and tr_A0A2H3TCG6_A0A2H3TCG6_FUSOX_5507 are exactly identical! WARNING: Sequences tr_E9FDQ0_E9FDQ0_METRA_655844 and tr_A0A0B4HI23_A0A0B4HI23_METMF_1276143 are exactly identical! WARNING: Sequences tr_E9FDQ0_E9FDQ0_METRA_655844 and tr_A0A0D9PBG1_A0A0D9PBG1_METAN_1291518 are exactly identical! WARNING: Sequences tr_Q2UEQ3_Q2UEQ3_ASPOR_510516 and tr_A0A1S9E0C1_A0A1S9E0C1_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A0E0I587_A0A0E0I587_ORYNI_4536 and tr_I1QCW4_I1QCW4_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A2QCE0_A2QCE0_ASPNC_425011 and tr_G3Y2A4_G3Y2A4_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2QCE0_A2QCE0_ASPNC_425011 and tr_A0A319AY71_A0A319AY71_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7X5J1_G7X5J1_ASPKW_1033177 and tr_A0A146FLF9_A0A146FLF9_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G2Y466_G2Y466_BOTF4_999810 and tr_M7UYS5_M7UYS5_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_B3RM53_B3RM53_TRIAD_10228 and tr_A0A369SIA7_A0A369SIA7_9METZ_287889 are exactly identical! WARNING: Sequences tr_G7PPA1_G7PPA1_MACFA_9541 and tr_A0A096N3W2_A0A096N3W2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7PPA1_G7PPA1_MACFA_9541 and tr_A0A0D9S3S3_A0A0D9S3S3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7PPA1_G7PPA1_MACFA_9541 and tr_A0A2K6CZ47_A0A2K6CZ47_MACNE_9545 are exactly identical! WARNING: Sequences tr_M2SBP8_M2SBP8_COCSN_665912 and tr_M2TNY8_M2TNY8_COCH5_701091 are exactly identical! WARNING: Sequences tr_U5H7Y6_U5H7Y6_USTV1_683840 and tr_A0A2X0N089_A0A2X0N089_9BASI_796604 are exactly identical! WARNING: Sequences tr_V2YTM8_V2YTM8_MONRO_1381753 and tr_A0A0W0EV90_A0A0W0EV90_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2PIP4_W2PIP4_PHYPN_761204 and tr_A0A0W8DLR7_A0A0W8DLR7_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A3B6ATW8_A0A3B6ATW8_WHEAT_4565 and tr_A0A3B6C100_A0A3B6C100_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A078H291_A0A078H291_BRANA_3708 and tr_A0A0D3BXD1_A0A0D3BXD1_BRAOL_109376 are exactly identical! WARNING: Sequences tr_A0A0V0S1G3_A0A0V0S1G3_9BILA_6336 and tr_A0A0V1CT46_A0A0V1CT46_TRIBR_45882 are exactly identical! WARNING: Sequences tr_A0A0V0S1G3_A0A0V0S1G3_9BILA_6336 and tr_A0A0V1LUN5_A0A0V1LUN5_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0S1G3_A0A0V0S1G3_9BILA_6336 and tr_A0A0V0UIG7_A0A0V0UIG7_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1CT88_A0A0V1CT88_TRIBR_45882 and tr_A0A0V0XBJ1_A0A0V0XBJ1_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1CT88_A0A0V1CT88_TRIBR_45882 and tr_A0A0V1LUT9_A0A0V1LUT9_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CT88_A0A0V1CT88_TRIBR_45882 and tr_A0A0V0UI72_A0A0V0UI72_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A100I520_A0A100I520_ASPNG_5061 and tr_A0A1L9NAS4_A0A1L9NAS4_ASPTU_767770 are exactly identical! WARNING: Duplicate sequences found: 33 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/Q9H3H5/4_raxmlng_ancestral/Q9H3H5.raxml.reduced.phy Alignment comprises 1 partitions and 408 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 408 Gaps: 10.78 % Invariant sites: 0.49 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9H3H5/4_raxmlng_ancestral/Q9H3H5.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/Q9H3H5/3_mltree/Q9H3H5.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 102 / 8160 [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: -185597.014605 [00:00:00 -185597.014605] Initial branch length optimization [00:00:01 -184939.972059] Model parameter optimization (eps = 0.100000) [00:00:41] Tree #1, final logLikelihood: -184226.363005 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.245355,0.337856) (0.350010,0.507391) (0.317867,1.462264) (0.086767,3.166025) 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/Q9H3H5/4_raxmlng_ancestral/Q9H3H5.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9H3H5/4_raxmlng_ancestral/Q9H3H5.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9H3H5/4_raxmlng_ancestral/Q9H3H5.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q9H3H5/4_raxmlng_ancestral/Q9H3H5.raxml.log Analysis started: 02-Jun-2021 18:36:11 / finished: 02-Jun-2021 18:36:57 Elapsed time: 45.459 seconds Consumed energy: 3.060 Wh