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 12-Jul-2021 17:36:02 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RP9/2_msa/Q96RP9_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RP9/3_mltree/Q96RP9.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RP9/4_raxmlng_ancestral/Q96RP9 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626100562 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/Q96RP9/2_msa/Q96RP9_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 751 sites WARNING: Sequences sp_B4Q5D5_EFGM_DROSI_7240 and sp_Q9VM33_EFGM_DROME_7227 are exactly identical! WARNING: Sequences sp_B4Q5D5_EFGM_DROSI_7240 and sp_B4HY41_EFGM_DROSE_7238 are exactly identical! WARNING: Sequences sp_Q1DLM0_EFGM_COCIM_246410 and tr_A0A0J6YHD4_A0A0J6YHD4_COCIT_404692 are exactly identical! WARNING: Sequences sp_B2WBM8_EFGM_PYRTR_426418 and tr_A0A2W1ETP0_A0A2W1ETP0_9PLEO_45151 are exactly identical! WARNING: Sequences tr_G3S1S5_G3S1S5_GORGO_9595 and tr_H2R7Y8_H2R7Y8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3S1S5_G3S1S5_GORGO_9595 and tr_A0A2R9AW37_A0A2R9AW37_PANPA_9597 are exactly identical! WARNING: Sequences sp_B8N9M2_EFGM_ASPFN_332952 and sp_Q2UGQ2_EFGM_ASPOR_510516 are exactly identical! WARNING: Sequences sp_B8N9M2_EFGM_ASPFN_332952 and tr_A0A1S9DZ16_A0A1S9DZ16_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179UFS4_A0A179UFS4_BLAGS_559298 and tr_C5GFF4_C5GFF4_AJEDR_559297 are exactly identical! WARNING: Sequences tr_F9FTJ9_F9FTJ9_FUSOF_660025 and tr_A0A0D2Y4X0_A0A0D2Y4X0_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FTJ9_F9FTJ9_FUSOF_660025 and tr_X0CSW1_X0CSW1_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FTJ9_F9FTJ9_FUSOF_660025 and tr_A0A2H3SUK9_A0A2H3SUK9_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FTJ9_F9FTJ9_FUSOF_660025 and tr_A0A2H3HRX7_A0A2H3HRX7_FUSOX_327505 are exactly identical! WARNING: Sequences tr_C6H211_C6H211_AJECH_544712 and tr_F0U4G6_F0U4G6_AJEC8_544711 are exactly identical! WARNING: Sequences tr_A0A0E0H3M3_A0A0E0H3M3_ORYNI_4536 and tr_A2XVY3_A2XVY3_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0H3M3_A0A0E0H3M3_ORYNI_4536 and tr_A0A0E0PC33_A0A0E0PC33_ORYRU_4529 are exactly identical! WARNING: Sequences sp_A2QI77_EFGM_ASPNC_425011 and tr_G3Y8R9_G3Y8R9_ASPNA_380704 are exactly identical! WARNING: Sequences sp_A2QI77_EFGM_ASPNC_425011 and tr_A0A319AHG1_A0A319AHG1_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7X7E8_G7X7E8_ASPKW_1033177 and tr_A0A146FI78_A0A146FI78_9EURO_1069201 are exactly identical! WARNING: Sequences tr_I1PCT5_I1PCT5_ORYGL_4538 and tr_A0A0D3FKH0_A0A0D3FKH0_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1PCT5_I1PCT5_ORYGL_4538 and sp_Q9FE64_EFGM_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1PNF0_I1PNF0_ORYGL_4538 and tr_A0A0D3FYE6_A0A0D3FYE6_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_I1PNF0_I1PNF0_ORYGL_4538 and tr_A0A0D9ZNL3_A0A0D9ZNL3_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_G2Y8S3_G2Y8S3_BOTF4_999810 and tr_M7U4F2_M7U4F2_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2SWJ7_F2SWJ7_TRIRC_559305 and tr_A0A178EYS4_A0A178EYS4_TRIRU_5551 are exactly identical! WARNING: Sequences tr_S0DKK9_S0DKK9_GIBF5_1279085 and tr_A0A2K0WAC8_A0A2K0WAC8_GIBNY_42673 are exactly identical! WARNING: Sequences tr_S0DKK9_S0DKK9_GIBF5_1279085 and tr_A0A365MSI9_A0A365MSI9_GIBIN_948311 are exactly identical! WARNING: Sequences tr_V2XFK5_V2XFK5_MONRO_1381753 and tr_A0A0W0G0G9_A0A0W0G0G9_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2QVP1_W2QVP1_PHYPN_761204 and tr_W2JZH9_W2JZH9_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A2X0S8T1_A0A2X0S8T1_WHEAT_4565 and tr_A0A3B6B1T9_A0A3B6B1T9_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A067H188_A0A067H188_CITSI_2711 and tr_V4U8R6_V4U8R6_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067H188_A0A067H188_CITSI_2711 and tr_A0A2H5NPL6_A0A2H5NPL6_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A094EQW3_A0A094EQW3_9PEZI_1420912 and tr_A0A1B8GS17_A0A1B8GS17_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0G4PBT0_A0A0G4PBT0_PENCA_1429867 and tr_A0A1V6NI72_A0A1V6NI72_9EURO_60169 are exactly identical! WARNING: Sequences tr_A0A164P9D4_A0A164P9D4_9HOMO_1314777 and tr_A0A165YQ21_A0A165YQ21_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A1U8EDZ1_A0A1U8EDZ1_CAPAN_4072 and tr_A0A2G3DJA4_A0A2G3DJA4_CAPCH_80379 are exactly identical! WARNING: Duplicate sequences found: 36 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/Q96RP9/4_raxmlng_ancestral/Q96RP9.raxml.reduced.phy Alignment comprises 1 partitions and 751 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 751 Gaps: 5.83 % Invariant sites: 2.80 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RP9/4_raxmlng_ancestral/Q96RP9.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/Q96RP9/3_mltree/Q96RP9.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 188 / 15040 [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: -268508.574221 [00:00:00 -268508.574221] Initial branch length optimization [00:00:01 -268282.717062] Model parameter optimization (eps = 0.100000) [00:00:40] Tree #1, final logLikelihood: -267690.031992 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.263634,0.257157) (0.332365,0.456881) (0.235301,1.220339) (0.168699,2.923578) 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/Q96RP9/4_raxmlng_ancestral/Q96RP9.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RP9/4_raxmlng_ancestral/Q96RP9.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RP9/4_raxmlng_ancestral/Q96RP9.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RP9/4_raxmlng_ancestral/Q96RP9.raxml.log Analysis started: 12-Jul-2021 17:36:02 / finished: 12-Jul-2021 17:36:49 Elapsed time: 47.485 seconds Consumed energy: 2.833 Wh