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 12-Jul-2021 18:19:37 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H2G2/2_msa/Q9H2G2_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H2G2/3_mltree/Q9H2G2.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H2G2/4_raxmlng_ancestral/Q9H2G2 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626103177 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/Q9H2G2/2_msa/Q9H2G2_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1235 sites WARNING: Sequences tr_A0A2I3G2I6_A0A2I3G2I6_NOMLE_61853 and tr_A0A2I3SVA8_A0A2I3SVA8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S3J1_G1S3J1_NOMLE_61853 and tr_H2P6F4_H2P6F4_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1S3J1_G1S3J1_NOMLE_61853 and tr_K7BKY5_K7BKY5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S3J1_G1S3J1_NOMLE_61853 and tr_H9EU76_H9EU76_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1S3J1_G1S3J1_NOMLE_61853 and tr_A0A2I3M2U3_A0A2I3M2U3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1S3J1_G1S3J1_NOMLE_61853 and tr_A0A0D9RJ11_A0A0D9RJ11_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1S3J1_G1S3J1_NOMLE_61853 and tr_A0A2K5MKX0_A0A2K5MKX0_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1S3J1_G1S3J1_NOMLE_61853 and tr_A0A2K6D539_A0A2K6D539_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1S3J1_G1S3J1_NOMLE_61853 and tr_A0A2R9AAI2_A0A2R9AAI2_PANPA_9597 are exactly identical! WARNING: Sequences tr_B6Q8M4_B6Q8M4_TALMQ_441960 and tr_A0A093VC69_A0A093VC69_TALMA_1077442 are exactly identical! WARNING: Sequences tr_Q290P0_Q290P0_DROPS_46245 and tr_B4GBG4_B4GBG4_DROPE_7234 are exactly identical! WARNING: Sequences tr_F6URD2_F6URD2_CANLF_9615 and tr_A0A2U3XFR8_A0A2U3XFR8_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2I3T3U0_A0A2I3T3U0_PANTR_9598 and tr_A0A2R8ZUF2_A0A2R8ZUF2_PANPA_9597 are exactly identical! WARNING: Sequences tr_H9ETH7_H9ETH7_MACMU_9544 and tr_A0A2K6B3Q6_A0A2K6B3Q6_MACNE_9545 are exactly identical! WARNING: Sequences tr_I1PFL5_I1PFL5_ORYGL_4538 and tr_A0A0D3FP84_A0A0D3FP84_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_G7PDW9_G7PDW9_MACFA_9541 and tr_A0A2K6C168_A0A2K6C168_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0JN96_A0JN96_BOVIN_9913 and tr_A0A1S3EVM6_A0A1S3EVM6_DIPOR_10020 are exactly identical! WARNING: Sequences tr_A0JN96_A0JN96_BOVIN_9913 and tr_A0A2U4AIA2_A0A2U4AIA2_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0JN96_A0JN96_BOVIN_9913 and tr_A0A2Y9PD37_A0A2Y9PD37_DELLE_9749 are exactly identical! WARNING: Sequences sp_E1BK52_STK10_BOVIN_9913 and tr_H2XJF0_H2XJF0_BOVIN_9913 are exactly identical! WARNING: Sequences tr_R1C5Q2_R1C5Q2_EMIHU_2903 and tr_R1DD94_R1DD94_EMIHU_2903 are exactly identical! WARNING: Sequences tr_A0A2K6VYR1_A0A2K6VYR1_ONCVO_6282 and tr_A0A182EDH7_A0A182EDH7_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A096NX80_A0A096NX80_PAPAN_9555 and tr_A0A0D9RP63_A0A0D9RP63_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096NX80_A0A096NX80_PAPAN_9555 and tr_A0A2K5YCM9_A0A2K5YCM9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A091J6U2_A0A091J6U2_EGRGA_188379 and tr_A0A093GFH4_A0A093GFH4_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091J6U2_A0A091J6U2_EGRGA_188379 and tr_A0A091J6Z5_A0A091J6Z5_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A0V0RVV3_A0A0V0RVV3_9BILA_6336 and tr_A0A0V1L179_A0A0V1L179_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A226MRR0_A0A226MRR0_CALSU_9009 and tr_A0A226PNG8_A0A226PNG8_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2K5L7J1_A0A2K5L7J1_CERAT_9531 and tr_A0A2K6B7S5_A0A2K6B7S5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K5L7J1_A0A2K5L7J1_CERAT_9531 and tr_A0A2K5XZ51_A0A2K5XZ51_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4BYP1_A0A2U4BYP1_TURTR_9739 and tr_A0A2Y9N633_A0A2Y9N633_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4C223_A0A2U4C223_TURTR_9739 and tr_A0A2Y9PXE7_A0A2Y9PXE7_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4C223_A0A2U4C223_TURTR_9739 and tr_A0A2Y9T1A9_A0A2Y9T1A9_PHYCD_9755 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/300621_run/phylogeny-snakemake/results/Q9H2G2/4_raxmlng_ancestral/Q9H2G2.raxml.reduced.phy Alignment comprises 1 partitions and 1235 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1235 Gaps: 45.49 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H2G2/4_raxmlng_ancestral/Q9H2G2.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/Q9H2G2/3_mltree/Q9H2G2.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 309 / 24720 [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: -374866.771152 [00:00:00 -374866.771152] Initial branch length optimization [00:00:02 -366411.195969] Model parameter optimization (eps = 0.100000) [00:01:47] Tree #1, final logLikelihood: -365387.595831 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.095390,0.148344) (0.071990,0.176124) (0.425737,0.591656) (0.406883,1.772698) 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/Q9H2G2/4_raxmlng_ancestral/Q9H2G2.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H2G2/4_raxmlng_ancestral/Q9H2G2.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H2G2/4_raxmlng_ancestral/Q9H2G2.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H2G2/4_raxmlng_ancestral/Q9H2G2.raxml.log Analysis started: 12-Jul-2021 18:19:37 / finished: 12-Jul-2021 18:21:36 Elapsed time: 119.229 seconds Consumed energy: 8.398 Wh