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 03-Jun-2021 02:27:35 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q68DV7/2_msa/Q68DV7_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q68DV7/3_mltree/Q68DV7.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q68DV7/4_raxmlng_ancestral/Q68DV7 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622676455 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/Q68DV7/2_msa/Q68DV7_nogap_msa.fasta [00:00:00] Loaded alignment with 1000 taxa and 783 sites WARNING: Sequences tr_G3QDA6_G3QDA6_GORGO_9595 and tr_H2QBZ2_H2QBZ2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QDA6_G3QDA6_GORGO_9595 and tr_A0A2R9BN69_A0A2R9BN69_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0E0GB76_A0A0E0GB76_ORYNI_4536 and tr_I1P326_I1P326_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0GB76_A0A0E0GB76_ORYNI_4536 and tr_A0A0E0CPQ6_A0A0E0CPQ6_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0GB76_A0A0E0GB76_ORYNI_4536 and tr_A0A0D3F8T3_A0A0D3F8T3_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A2XDD3_A2XDD3_ORYSI_39946 and tr_A0A0E0NQT0_A0A0E0NQT0_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A2XDD3_A2XDD3_ORYSI_39946 and sp_Q8H7N9_ATL31_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_B8AKR0_B8AKR0_ORYSI_39946 and tr_I1P9Y0_I1P9Y0_ORYGL_4538 are exactly identical! WARNING: Sequences tr_B8AKR0_B8AKR0_ORYSI_39946 and tr_Q10NE1_Q10NE1_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1P8C9_I1P8C9_ORYGL_4538 and tr_A0A0D3FET1_A0A0D3FET1_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0NJ48_A0A0E0NJ48_ORYRU_4529 and tr_Q0DYQ7_Q0DYQ7_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0NT78_A0A0E0NT78_ORYRU_4529 and tr_A0A0D9Z596_A0A0D9Z596_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_G7PF67_G7PF67_MACFA_9541 and tr_A0A0D9RAR2_A0A0D9RAR2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7PT98_G7PT98_MACFA_9541 and tr_A0A2K5LHF8_A0A2K5LHF8_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PT98_G7PT98_MACFA_9541 and tr_A0A2K6CA94_A0A2K6CA94_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PT98_G7PT98_MACFA_9541 and tr_A0A2K5ZPG2_A0A2K5ZPG2_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A015IC27_A0A015IC27_9GLOM_1432141 and tr_A0A2H5SSM0_A0A2H5SSM0_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A067G361_A0A067G361_CITSI_2711 and tr_V4UFL5_V4UFL5_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A078IHG0_A0A078IHG0_BRANA_3708 and tr_A0A0D3D3E7_A0A0D3D3E7_BRAOL_109376 are exactly identical! WARNING: Sequences tr_V4TCG9_V4TCG9_9ROSI_85681 and tr_A0A2H5NYN5_A0A2H5NYN5_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0D2N4C1_A0A0D2N4C1_GOSRA_29730 and tr_A0A1U8LYS1_A0A1U8LYS1_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2SKI4_A0A0D2SKI4_GOSRA_29730 and tr_A0A1U8M8K8_A0A1U8M8K8_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2TE72_A0A0D2TE72_GOSRA_29730 and tr_A0A1U8LR34_A0A1U8LR34_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A091JJI8_A0A091JJI8_EGRGA_188379 and tr_A0A091WPC6_A0A091WPC6_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A1S3XVN0_A0A1S3XVN0_TOBAC_4097 and tr_A0A1U7V4Z4_A0A1U7V4Z4_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3Z394_A0A1S3Z394_TOBAC_4097 and tr_A0A1U7YMY5_A0A1U7YMY5_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3ZG30_A0A1S3ZG30_TOBAC_4097 and tr_A0A314KHY7_A0A314KHY7_NICAT_49451 are exactly identical! WARNING: Sequences tr_A0A1S3ZG30_A0A1S3ZG30_TOBAC_4097 and tr_A0A1U7Y143_A0A1U7Y143_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4DDC3_A0A1S4DDC3_TOBAC_4097 and tr_A0A1U7W516_A0A1U7W516_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2D0QB05_A0A2D0QB05_ICTPU_7998 and tr_A0A2D0QC58_A0A2D0QC58_ICTPU_7998 are exactly identical! WARNING: Duplicate sequences found: 30 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/Q68DV7/4_raxmlng_ancestral/Q68DV7.raxml.reduced.phy Alignment comprises 1 partitions and 783 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 783 Gaps: 65.60 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q68DV7/4_raxmlng_ancestral/Q68DV7.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/Q68DV7/3_mltree/Q68DV7.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 196 / 15680 [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: -258850.867359 [00:00:00 -258850.867359] Initial branch length optimization [00:00:02 -210550.342237] Model parameter optimization (eps = 0.100000) [00:01:17] Tree #1, final logLikelihood: -210138.132086 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.049247,0.139155) (0.035752,0.224673) (0.422527,0.636479) (0.492474,1.454260) 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/Q68DV7/4_raxmlng_ancestral/Q68DV7.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q68DV7/4_raxmlng_ancestral/Q68DV7.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q68DV7/4_raxmlng_ancestral/Q68DV7.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q68DV7/4_raxmlng_ancestral/Q68DV7.raxml.log Analysis started: 03-Jun-2021 02:27:35 / finished: 03-Jun-2021 02:28:59 Elapsed time: 84.562 seconds Consumed energy: 3.765 Wh