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 18:14:06 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6ZMI3/2_msa/Q6ZMI3_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6ZMI3/3_mltree/Q6ZMI3.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6ZMI3/4_raxmlng_ancestral/Q6ZMI3 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626102846 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/Q6ZMI3/2_msa/Q6ZMI3_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 551 sites WARNING: Sequences sp_Q9IAK4_NOE1_CHICK_9031 and tr_H0Z6H8_H0Z6H8_TAEGU_59729 are exactly identical! WARNING: Sequences sp_Q9IAK4_NOE1_CHICK_9031 and tr_U3JG49_U3JG49_FICAL_59894 are exactly identical! WARNING: Sequences sp_Q9IAK4_NOE1_CHICK_9031 and tr_A0A1U7S3P9_A0A1U7S3P9_ALLSI_38654 are exactly identical! WARNING: Sequences sp_Q9IAK4_NOE1_CHICK_9031 and tr_A0A1V4J5Y9_A0A1V4J5Y9_PATFA_372326 are exactly identical! WARNING: Sequences sp_Q9IAK4_NOE1_CHICK_9031 and tr_A0A218V6G4_A0A218V6G4_9PASE_299123 are exactly identical! WARNING: Sequences sp_Q9IAK4_NOE1_CHICK_9031 and tr_A0A226NMR4_A0A226NMR4_CALSU_9009 are exactly identical! WARNING: Sequences tr_G3QJ50_G3QJ50_GORGO_9595 and tr_H2QJP2_H2QJP2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QJ50_G3QJ50_GORGO_9595 and sp_P12111_CO6A3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QT74_G3QT74_GORGO_9595 and tr_A0A2I3T087_A0A2I3T087_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2R1M0_H2R1M0_PANTR_9598 and sp_Q99784_NOE1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2R1M0_H2R1M0_PANTR_9598 and tr_A0A2R8PE66_A0A2R8PE66_CALJA_9483 are exactly identical! WARNING: Sequences tr_H2R1M0_H2R1M0_PANTR_9598 and tr_A0A2I3LPX1_A0A2I3LPX1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A3B5QSY9_A0A3B5QSY9_XIPMA_8083 and tr_A0A087Y2U8_A0A087Y2U8_POEFO_48698 are exactly identical! WARNING: Sequences sp_P12110_CO6A2_HUMAN_9606 and tr_A0A2R9A7P8_A0A2R9A7P8_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5QCB9_A0A1D5QCB9_MACMU_9544 and tr_A0A2K6CHL5_A0A2K6CHL5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6XD59_F6XD59_MACMU_9544 and tr_A0A2K5NK39_A0A2K5NK39_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6XD59_F6XD59_MACMU_9544 and tr_A0A2K6CKR7_A0A2K6CKR7_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FPW3_F7FPW3_MACMU_9544 and tr_A0A2K5MIM6_A0A2K5MIM6_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7FPW3_F7FPW3_MACMU_9544 and tr_A0A2K6B809_A0A2K6B809_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FPW3_F7FPW3_MACMU_9544 and tr_A0A2K5YA30_A0A2K5YA30_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7FYZ2_F7FYZ2_MACMU_9544 and tr_A0A2K6CSK8_A0A2K6CSK8_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3N198_A0A2I3N198_PAPAN_9555 and tr_A0A0D9RZL4_A0A0D9RZL4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3N198_A0A2I3N198_PAPAN_9555 and tr_A0A2K5M607_A0A2K5M607_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3NA02_A0A2I3NA02_PAPAN_9555 and tr_A0A2K5LIV9_A0A2K5LIV9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A151MFU1_A0A151MFU1_ALLMI_8496 and tr_A0A2I0M3M4_A0A2I0M3M4_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A091F9S6_A0A091F9S6_CORBR_85066 and tr_A0A091JG19_A0A091JG19_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A091F9S6_A0A091F9S6_CORBR_85066 and tr_A0A093SM45_A0A093SM45_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091F9S6_A0A091F9S6_CORBR_85066 and tr_A0A091VTL0_A0A091VTL0_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091F9S6_A0A091F9S6_CORBR_85066 and tr_A0A087R4Q6_A0A087R4Q6_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091F9S6_A0A091F9S6_CORBR_85066 and tr_A0A093JB84_A0A093JB84_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091F9S6_A0A091F9S6_CORBR_85066 and tr_A0A091XVL2_A0A091XVL2_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091F9S6_A0A091F9S6_CORBR_85066 and tr_A0A099ZKC3_A0A099ZKC3_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A091F9S6_A0A091F9S6_CORBR_85066 and tr_A0A0A0B119_A0A0A0B119_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A226MTY1_A0A226MTY1_CALSU_9009 and tr_A0A226PPF8_A0A226PPF8_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0QP39_A0A2D0QP39_ICTPU_7998 and tr_A0A2D0QQS3_A0A2D0QQS3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QP39_A0A2D0QP39_ICTPU_7998 and tr_A0A2D0QRG5_A0A2D0QRG5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5KM30_A0A2K5KM30_CERAT_9531 and tr_A0A2K5YW92_A0A2K5YW92_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U3WNV9_A0A2U3WNV9_ODORO_9708 and tr_A0A2U3Y7J1_A0A2U3Y7J1_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 38 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/Q6ZMI3/4_raxmlng_ancestral/Q6ZMI3.raxml.reduced.phy Alignment comprises 1 partitions and 551 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 551 Gaps: 48.80 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6ZMI3/4_raxmlng_ancestral/Q6ZMI3.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/Q6ZMI3/3_mltree/Q6ZMI3.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 138 / 11040 [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: -236058.454085 [00:00:00 -236058.454085] Initial branch length optimization [00:00:02 -205427.401616] Model parameter optimization (eps = 0.100000) [00:01:14] Tree #1, final logLikelihood: -204575.067500 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.128304,0.950369) (0.164854,0.682020) (0.262728,0.631412) (0.444113,1.350421) 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/Q6ZMI3/4_raxmlng_ancestral/Q6ZMI3.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6ZMI3/4_raxmlng_ancestral/Q6ZMI3.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6ZMI3/4_raxmlng_ancestral/Q6ZMI3.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6ZMI3/4_raxmlng_ancestral/Q6ZMI3.raxml.log Analysis started: 12-Jul-2021 18:14:06 / finished: 12-Jul-2021 18:15:26 Elapsed time: 80.292 seconds Consumed energy: 7.040 Wh