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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 17-Jun-2021 23:59:18 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P69892/2_msa/P69892_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P69892/3_mltree/P69892.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P69892/4_raxmlng_ancestral/P69892 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1623963558 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/P69892/2_msa/P69892_nogap_msa.fasta [00:00:00] Loaded alignment with 901 taxa and 147 sites WARNING: Sequences tr_F6P731_F6P731_DANRE_7955 and tr_Q7ZT21_Q7ZT21_DANRE_7955 are exactly identical! WARNING: Sequences tr_G1S6C6_G1S6C6_NOMLE_61853 and sp_P61773_HBD_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S6C6_G1S6C6_NOMLE_61853 and sp_P61772_HBD_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S6C6_G1S6C6_NOMLE_61853 and tr_A0A2R9AC19_A0A2R9AC19_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QY87_G3QY87_GORGO_9595 and tr_H2NPI6_H2NPI6_PONAB_9601 are exactly identical! WARNING: Sequences sp_P62742_HBG2_GORGO_9595 and sp_P61921_HBG2_PANTR_9598 are exactly identical! WARNING: Sequences sp_P62742_HBG2_GORGO_9595 and sp_P69892_HBG2_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q6LDH0_HBE_GORGO_9595 and sp_Q6LDH1_HBE_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q6LDH0_HBE_GORGO_9595 and sp_P02100_HBE_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q6LDH0_HBE_GORGO_9595 and tr_A0A2R9BP35_A0A2R9BP35_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1U9Q8_G1U9Q8_MELGA_9103 and tr_A0A226MDR3_A0A226MDR3_CALSU_9009 are exactly identical! WARNING: Sequences tr_G1U9Q8_G1U9Q8_MELGA_9103 and tr_A0A226P0J4_A0A226P0J4_COLVI_9014 are exactly identical! WARNING: Sequences tr_G1TPE2_G1TPE2_RABIT_9986 and sp_P02103_HBE_RABIT_9986 are exactly identical! WARNING: Sequences tr_J9JHW7_J9JHW7_CANLF_9615 and tr_J9P710_J9P710_CANLF_9615 are exactly identical! WARNING: Sequences tr_A0A2I3SN30_A0A2I3SN30_PANTR_9598 and sp_P09105_HBAT_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3SN30_A0A2I3SN30_PANTR_9598 and tr_A0A2R9BK37_A0A2R9BK37_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R1M1_H2R1M1_PANTR_9598 and tr_A0A2R8ZJR3_A0A2R8ZJR3_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R5L8_H2R5L8_PANTR_9598 and sp_Q28779_HBG1_PANPA_9597 are exactly identical! WARNING: Sequences sp_P06347_HBAZ_PANTR_9598 and tr_A0A2R8ZJQ4_A0A2R8ZJQ4_PANPA_9597 are exactly identical! WARNING: Sequences sp_P61920_HBG1_PANTR_9598 and sp_P69891_HBG1_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P68873_HBB_PANTR_9598 and sp_P68871_HBB_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P68873_HBB_PANTR_9598 and sp_P68872_HBB_PANPA_9597 are exactly identical! WARNING: Sequences sp_P69907_HBA_PANTR_9598 and sp_P69905_HBA_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P69907_HBA_PANTR_9598 and sp_P69906_HBA_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7AV81_F7AV81_MACMU_9544 and tr_G7PQY3_G7PQY3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7AV81_F7AV81_MACMU_9544 and sp_P68225_HBB_MACNE_9545 are exactly identical! WARNING: Sequences sp_P68077_HBG_MACMU_9544 and tr_A9L8Y0_A9L8Y0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6WIM6_F6WIM6_CALJA_9483 and sp_Q9GJS7_HBG_CALJA_9483 are exactly identical! WARNING: Sequences tr_A9L8U0_A9L8U0_PAPAN_9555 and tr_A0A2K5MX97_A0A2K5MX97_CERAT_9531 are exactly identical! WARNING: Sequences tr_A9L8U0_A9L8U0_PAPAN_9555 and tr_A0A2K6CQE3_A0A2K6CQE3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1U7TAR4_A0A1U7TAR4_TARSY_1868482 and sp_P13558_HBD_TARSY_1868482 are exactly identical! WARNING: Sequences tr_A0A1U7TD49_A0A1U7TD49_TARSY_1868482 and sp_P13557_HBB_TARSY_1868482 are exactly identical! WARNING: Sequences tr_A0A1U7Q945_A0A1U7Q945_MESAU_10036 and sp_P29626_HBBY_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A226MB68_A0A226MB68_CALSU_9009 and tr_A0A226P3X1_A0A226P3X1_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0S6B3_A0A2D0S6B3_ICTPU_7998 and tr_W5U988_W5U988_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5KYI6_A0A2K5KYI6_CERAT_9531 and tr_A0A2K5YN23_A0A2K5YN23_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K6DGR3_A0A2K6DGR3_MACNE_9545 and tr_A0A2K5XF24_A0A2K5XF24_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A1K0FUE0_A0A1K0FUE0_TURTR_9739 and tr_A0A2Y9PT12_A0A2Y9PT12_DELLE_9749 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/020621_run/phylogeny-snakemake/results/P69892/4_raxmlng_ancestral/P69892.raxml.reduced.phy Alignment comprises 1 partitions and 147 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 147 Gaps: 5.84 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P69892/4_raxmlng_ancestral/P69892.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/P69892/3_mltree/P69892.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 37 / 2960 [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: -57107.327449 [00:00:00 -57107.327449] Initial branch length optimization [00:00:00 -57012.180893] Model parameter optimization (eps = 0.100000) [00:00:21] Tree #1, final logLikelihood: -56712.735749 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.217926,0.694499) (0.228306,0.614652) (0.368931,0.932883) (0.184837,1.970128) 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/P69892/4_raxmlng_ancestral/P69892.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P69892/4_raxmlng_ancestral/P69892.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P69892/4_raxmlng_ancestral/P69892.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P69892/4_raxmlng_ancestral/P69892.raxml.log Analysis started: 17-Jun-2021 23:59:18 / finished: 17-Jun-2021 23:59:41 Elapsed time: 23.274 seconds Consumed energy: 1.693 Wh