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 14:59:16 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q92743/2_msa/Q92743_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q92743/3_mltree/Q92743.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q92743/4_raxmlng_ancestral/Q92743 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622721556 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/Q92743/2_msa/Q92743_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 480 sites WARNING: Sequences sp_B4QZU6_HTRA2_DROSI_7240 and sp_B4HEM8_HTRA2_DROSE_7238 are exactly identical! WARNING: Sequences tr_D8QTR3_D8QTR3_SELML_88036 and tr_D8T3S3_D8T3S3_SELML_88036 are exactly identical! WARNING: Sequences tr_A0A2I3S9Y1_A0A2I3S9Y1_PANTR_9598 and tr_A0A2R9CCL7_A0A2R9CCL7_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A088AMU0_A0A088AMU0_APIME_7460 and tr_A0A2A3EDE7_A0A2A3EDE7_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NUD5_A0A158NUD5_ATTCE_12957 and tr_A0A195BEW1_A0A195BEW1_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A0E0HIM5_A0A0E0HIM5_ORYNI_4536 and tr_B8AWT0_B8AWT0_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0JCJ2_A0A0E0JCJ2_ORYNI_4536 and tr_A2ZMS2_A2ZMS2_ORYSI_39946 are exactly identical! WARNING: Sequences tr_F6UNR7_F6UNR7_MACMU_9544 and tr_A0A0D9RT82_A0A0D9RT82_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6UNR7_F6UNR7_MACMU_9544 and tr_A0A2K6E6B7_A0A2K6E6B7_MACNE_9545 are exactly identical! WARNING: Sequences tr_B8AY70_B8AY70_ORYSI_39946 and tr_I1PSF5_I1PSF5_ORYGL_4538 are exactly identical! WARNING: Sequences tr_B8AY70_B8AY70_ORYSI_39946 and tr_Q6ASR0_Q6ASR0_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1PY26_I1PY26_ORYGL_4538 and tr_A0A0D3GAZ7_A0A0D3GAZ7_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0PRE4_A0A0E0PRE4_ORYRU_4529 and tr_Q6AUN5_Q6AUN5_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0R6D1_A0A0E0R6D1_ORYRU_4529 and tr_A0A0E0BHA0_A0A0E0BHA0_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_W2QD27_W2QD27_PHYPN_761204 and tr_A0A0W8AZ63_A0A0W8AZ63_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A096NU19_A0A096NU19_PAPAN_9555 and tr_A0A2K6D810_A0A2K6D810_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A078J0A3_A0A078J0A3_BRANA_3708 and tr_A0A0D3DBZ4_A0A0D3DBZ4_BRAOL_109376 are exactly identical! WARNING: Sequences tr_V4U8K1_V4U8K1_9ROSI_85681 and tr_A0A2H5N1J0_A0A2H5N1J0_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0D2SY68_A0A0D2SY68_GOSRA_29730 and tr_A0A1U8LRJ0_A0A1U8LRJ0_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2SY68_A0A0D2SY68_GOSRA_29730 and tr_A0A1U8MHS2_A0A1U8MHS2_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2TAU2_A0A0D2TAU2_GOSRA_29730 and tr_A0A1U8K3L4_A0A1U8K3L4_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2TAU2_A0A0D2TAU2_GOSRA_29730 and tr_A0A1U8L1H0_A0A1U8L1H0_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A091JPE4_A0A091JPE4_EGRGA_188379 and tr_A0A091X1U8_A0A091X1U8_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JPE4_A0A091JPE4_EGRGA_188379 and tr_A0A0A0AAM4_A0A0A0AAM4_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V1CX37_A0A0V1CX37_TRIBR_45882 and tr_A0A0V1PGS5_A0A0V1PGS5_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A1S3YCL4_A0A1S3YCL4_TOBAC_4097 and tr_A0A1U7YGZ4_A0A1U7YGZ4_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3YK97_A0A1S3YK97_TOBAC_4097 and tr_A0A1U7WWH4_A0A1U7WWH4_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4CNY8_A0A1S4CNY8_TOBAC_4097 and tr_A0A1U7WY41_A0A1U7WY41_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3Q335_A0A1S3Q335_SALSA_8030 and tr_B5X160_B5X160_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A2U4ART3_A0A2U4ART3_TURTR_9739 and tr_A0A2Y9M9T2_A0A2Y9M9T2_DELLE_9749 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/Q92743/4_raxmlng_ancestral/Q92743.raxml.reduced.phy Alignment comprises 1 partitions and 480 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 480 Gaps: 32.68 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q92743/4_raxmlng_ancestral/Q92743.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/Q92743/3_mltree/Q92743.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 120 / 9600 [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: -193353.068477 [00:00:00 -193353.068477] Initial branch length optimization [00:00:00 -191284.011308] Model parameter optimization (eps = 0.100000) [00:00:34] Tree #1, final logLikelihood: -190538.166603 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.143380,0.288419) (0.143124,0.304539) (0.313614,0.706997) (0.399882,1.733852) 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/Q92743/4_raxmlng_ancestral/Q92743.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q92743/4_raxmlng_ancestral/Q92743.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q92743/4_raxmlng_ancestral/Q92743.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q92743/4_raxmlng_ancestral/Q92743.raxml.log Analysis started: 03-Jun-2021 14:59:16 / finished: 03-Jun-2021 14:59:54 Elapsed time: 38.285 seconds Consumed energy: 3.116 Wh