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 17:49:11 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O60243/2_msa/O60243_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O60243/3_mltree/O60243.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O60243/4_raxmlng_ancestral/O60243 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626101351 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/O60243/2_msa/O60243_nogap_msa.fasta [00:00:00] Loaded alignment with 503 taxa and 411 sites WARNING: Sequences tr_B4QSR8_B4QSR8_DROSI_7240 and tr_Q9VDR6_Q9VDR6_DROME_7227 are exactly identical! WARNING: Sequences tr_G1S1F9_G1S1F9_NOMLE_61853 and tr_A0A2I2YYD2_A0A2I2YYD2_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S1F9_G1S1F9_NOMLE_61853 and tr_H2P789_H2P789_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1S1F9_G1S1F9_NOMLE_61853 and tr_H2QIP8_H2QIP8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S1F9_G1S1F9_NOMLE_61853 and sp_O60243_H6ST1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1S1F9_G1S1F9_NOMLE_61853 and tr_A0A096NRW6_A0A096NRW6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1S1F9_G1S1F9_NOMLE_61853 and tr_A0A2K5M7L0_A0A2K5M7L0_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1S1F9_G1S1F9_NOMLE_61853 and tr_A0A2K6BEF9_A0A2K6BEF9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1SBP7_G1SBP7_NOMLE_61853 and tr_F6TT40_F6TT40_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1SBP7_G1SBP7_NOMLE_61853 and tr_A0A2K5XT30_A0A2K5XT30_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3RE22_G3RE22_GORGO_9595 and tr_A0A2J8JSL9_A0A2J8JSL9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RE22_G3RE22_GORGO_9595 and tr_A0A2R9AL13_A0A2R9AL13_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A087ZVC4_A0A087ZVC4_APIME_7460 and tr_A0A2A3E821_A0A2A3E821_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A0K0JMU7_A0A0K0JMU7_BRUMA_6279 and tr_A0A0R3QV16_A0A0R3QV16_9BILA_42155 are exactly identical! WARNING: Sequences tr_F6Z463_F6Z463_MACMU_9544 and tr_A0A096MMZ8_A0A096MMZ8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6Z463_F6Z463_MACMU_9544 and tr_A0A2K5KXF2_A0A2K5KXF2_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6Z463_F6Z463_MACMU_9544 and tr_A0A2K6D410_A0A2K6D410_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096NEL8_A0A096NEL8_PAPAN_9555 and tr_A0A2K5M6Q3_A0A2K5M6Q3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NEL8_A0A096NEL8_PAPAN_9555 and tr_A0A2K6DAE1_A0A2K6DAE1_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A091EH64_A0A091EH64_CORBR_85066 and tr_A0A091J9Y3_A0A091J9Y3_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A091EH64_A0A091EH64_CORBR_85066 and tr_A0A093QQH7_A0A093QQH7_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091EH64_A0A091EH64_CORBR_85066 and tr_A0A091USM5_A0A091USM5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091EH64_A0A091EH64_CORBR_85066 and tr_A0A087RBT9_A0A087RBT9_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091EH64_A0A091EH64_CORBR_85066 and tr_A0A093HI10_A0A093HI10_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091EH64_A0A091EH64_CORBR_85066 and tr_A0A091W0T9_A0A091W0T9_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091EH64_A0A091EH64_CORBR_85066 and tr_A0A091GLE5_A0A091GLE5_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091EH64_A0A091EH64_CORBR_85066 and tr_A0A099ZWF3_A0A099ZWF3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091EH64_A0A091EH64_CORBR_85066 and tr_A0A093GL65_A0A093GL65_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A226MP68_A0A226MP68_CALSU_9009 and tr_A0A226PK94_A0A226PK94_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226MU32_A0A226MU32_CALSU_9009 and tr_A0A226PTI2_A0A226PTI2_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NIP2_A0A226NIP2_CALSU_9009 and tr_A0A226PHZ5_A0A226PHZ5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U4A1L7_A0A2U4A1L7_TURTR_9739 and tr_A0A2Y9MKT9_A0A2Y9MKT9_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3VZQ2_A0A2U3VZQ2_ODORO_9708 and tr_A0A2Y9LEL8_A0A2Y9LEL8_ENHLU_391180 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/O60243/4_raxmlng_ancestral/O60243.raxml.reduced.phy Alignment comprises 1 partitions and 411 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 411 Gaps: 30.49 % Invariant sites: 0.24 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O60243/4_raxmlng_ancestral/O60243.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/O60243/3_mltree/O60243.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 103 / 8240 [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: -60015.429065 [00:00:00 -60015.429065] Initial branch length optimization [00:00:00 -58589.949711] Model parameter optimization (eps = 0.100000) [00:00:16] Tree #1, final logLikelihood: -58325.860747 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.248401,0.322219) (0.179348,0.737430) (0.323568,0.873024) (0.248683,2.031589) 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/O60243/4_raxmlng_ancestral/O60243.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O60243/4_raxmlng_ancestral/O60243.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O60243/4_raxmlng_ancestral/O60243.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O60243/4_raxmlng_ancestral/O60243.raxml.log Analysis started: 12-Jul-2021 17:49:11 / finished: 12-Jul-2021 17:49:29 Elapsed time: 18.531 seconds Consumed energy: 1.380 Wh