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 18:02:34 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCS5/2_msa/Q9HCS5_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCS5/3_mltree/Q9HCS5.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCS5/4_raxmlng_ancestral/Q9HCS5 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626102154 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/Q9HCS5/2_msa/Q9HCS5_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 686 sites WARNING: Sequences tr_B4R188_B4R188_DROSI_7240 and tr_B4HFS6_B4HFS6_DROSE_7238 are exactly identical! WARNING: Sequences tr_G3QZL4_G3QZL4_GORGO_9595 and tr_H2QTQ8_H2QTQ8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QZL4_G3QZL4_GORGO_9595 and sp_O43491_E41L2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QZL4_G3QZL4_GORGO_9595 and tr_A0A2R9A1P9_A0A2R9A1P9_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RLI5_G3RLI5_GORGO_9595 and tr_H2Q9B7_H2Q9B7_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RLI5_G3RLI5_GORGO_9595 and sp_Q7Z6J6_FRMD5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RLI5_G3RLI5_GORGO_9595 and tr_A0A2R9AYL7_A0A2R9AYL7_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3SFI6_G3SFI6_GORGO_9595 and tr_A0A2I3RMK9_A0A2I3RMK9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SFI6_G3SFI6_GORGO_9595 and sp_Q9H4G0_E41L1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3SFI6_G3SFI6_GORGO_9595 and tr_A0A2R9AYJ0_A0A2R9AYJ0_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8JCK6_A0A2J8JCK6_PANTR_9598 and sp_P11171_41_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8JCK6_A0A2J8JCK6_PANTR_9598 and tr_A0A2R9BLM6_A0A2R9BLM6_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QE82_H2QE82_PANTR_9598 and tr_A0A2R9AJB0_A0A2R9AJB0_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QRB4_H2QRB4_PANTR_9598 and tr_A0A2R9C1I3_A0A2R9C1I3_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A158NJY3_A0A158NJY3_ATTCE_12957 and tr_F4WIK9_F4WIK9_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A1D5QMD8_A0A1D5QMD8_MACMU_9544 and tr_A0A2K6BU75_A0A2K6BU75_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6WK37_F6WK37_MACMU_9544 and tr_G7PN58_G7PN58_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6WK37_F6WK37_MACMU_9544 and tr_A0A096MX43_A0A096MX43_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6WK37_F6WK37_MACMU_9544 and tr_A0A0D9RVP8_A0A0D9RVP8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6WK37_F6WK37_MACMU_9544 and tr_A0A2K6CIJ0_A0A2K6CIJ0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6WK37_F6WK37_MACMU_9544 and tr_A0A2K5ZW56_A0A2K5ZW56_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7NKD7_G7NKD7_MACMU_9544 and tr_G7PWE9_G7PWE9_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7NKD7_G7NKD7_MACMU_9544 and tr_A0A2K5MF59_A0A2K5MF59_CERAT_9531 are exactly identical! WARNING: Sequences tr_A8X7Z5_A8X7Z5_CAEBR_6238 and tr_A0A2G5USK9_A0A2G5USK9_9PELO_1611254 are exactly identical! WARNING: Sequences tr_G1LU01_G1LU01_AILME_9646 and tr_A0A384CNE7_A0A384CNE7_URSMA_29073 are exactly identical! WARNING: Sequences tr_G7P821_G7P821_MACFA_9541 and tr_A0A2K6CA35_A0A2K6CA35_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PB80_G7PB80_MACFA_9541 and tr_A0A0D9RAY5_A0A0D9RAY5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G8F3Y8_G8F3Y8_MACFA_9541 and tr_A0A2K5LAS1_A0A2K5LAS1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3M5V1_A0A2I3M5V1_PAPAN_9555 and tr_A0A2K5NGU0_A0A2K5NGU0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3M5V1_A0A2I3M5V1_PAPAN_9555 and tr_A0A2K6A326_A0A2K6A326_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3M9B9_A0A2I3M9B9_PAPAN_9555 and tr_A0A2K5MLF7_A0A2K5MLF7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3M9B9_A0A2I3M9B9_PAPAN_9555 and tr_A0A2K6BDC5_A0A2K6BDC5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A091JIF4_A0A091JIF4_EGRGA_188379 and tr_A0A091VF77_A0A091VF77_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A087R3U9_A0A087R3U9_APTFO_9233 and tr_A0A0A0AKQ9_A0A0A0AKQ9_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V1DD14_A0A0V1DD14_TRIBR_45882 and tr_A0A0V1PJP1_A0A0V1PJP1_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1DD14_A0A0V1DD14_TRIBR_45882 and tr_A0A0V0UE85_A0A0V0UE85_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0W710_A0A0V0W710_9BILA_92179 and tr_A0A0V1KV56_A0A0V1KV56_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A1S3AFI9_A0A1S3AFI9_ERIEU_9365 and tr_A0A2U3ZRV3_A0A2U3ZRV3_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A1S3AFI9_A0A1S3AFI9_ERIEU_9365 and tr_A0A2U3X7Q5_A0A2U3X7Q5_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A226N5E6_A0A226N5E6_CALSU_9009 and tr_A0A226PCE9_A0A226PCE9_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0R2I7_A0A2D0R2I7_ICTPU_7998 and tr_A0A2D0R404_A0A2D0R404_ICTPU_7998 are exactly identical! WARNING: Duplicate sequences found: 41 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/Q9HCS5/4_raxmlng_ancestral/Q9HCS5.raxml.reduced.phy Alignment comprises 1 partitions and 686 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 686 Gaps: 27.21 % Invariant sites: 0.15 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCS5/4_raxmlng_ancestral/Q9HCS5.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/Q9HCS5/3_mltree/Q9HCS5.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 172 / 13760 [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: -219584.524460 [00:00:00 -219584.524460] Initial branch length optimization [00:00:01 -194825.695767] Model parameter optimization (eps = 0.100000) [00:00:38] Tree #1, final logLikelihood: -194444.921684 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.114118,0.178205) (0.125153,0.244743) (0.274980,0.623462) (0.485749,1.600814) 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/Q9HCS5/4_raxmlng_ancestral/Q9HCS5.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCS5/4_raxmlng_ancestral/Q9HCS5.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCS5/4_raxmlng_ancestral/Q9HCS5.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9HCS5/4_raxmlng_ancestral/Q9HCS5.raxml.log Analysis started: 12-Jul-2021 18:02:34 / finished: 12-Jul-2021 18:03:18 Elapsed time: 44.199 seconds Consumed energy: 3.513 Wh