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 18:15:29 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RK1/2_msa/Q96RK1_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RK1/3_mltree/Q96RK1.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RK1/4_raxmlng_ancestral/Q96RK1 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626102929 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/Q96RK1/2_msa/Q96RK1_nogap_msa.fasta [00:00:00] Loaded alignment with 226 taxa and 184 sites WARNING: Sequences sp_Q9I8K7_CITE3_CHICK_9031 and tr_G1NRH9_G1NRH9_MELGA_9103 are exactly identical! WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_G3RJ28_G3RJ28_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_A0A2J8X9X6_A0A2J8X9X6_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_A0A2I3SY88_A0A2I3SY88_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_Q99MA1_Q99MA1_RAT_10116 are exactly identical! WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_I3MBV1_I3MBV1_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_H0V0R6_H0V0R6_CAVPO_10141 are exactly identical! WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and sp_Q99967_CITE2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_A0A1D5QPF9_A0A1D5QPF9_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_A0A2R8P6R0_A0A2R8P6R0_CALJA_9483 are exactly identical! WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_L5KDA0_L5KDA0_PTEAL_9402 are exactly identical! WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_M3X852_M3X852_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_A0A0D9SAC0_A0A0D9SAC0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_A0A1U7Q8B9_A0A1U7Q8B9_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_A0A2K5LUA5_A0A2K5LUA5_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_A0A2K6D2U1_A0A2K6D2U1_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_A0A2K5Y5Z7_A0A2K5Y5Z7_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_A0A2U3WMT0_A0A2U3WMT0_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_A0A2U3YZF2_A0A2U3YZF2_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3Z5A2_M3Z5A2_MUSPF_9669 and tr_A0A2Y9JGV1_A0A2Y9JGV1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_H2PW07_H2PW07_PONAB_9601 and tr_A0A2J8IVZ1_A0A2J8IVZ1_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2PW07_H2PW07_PONAB_9601 and tr_A0A2R9BGL8_A0A2R9BGL8_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6VSF3_F6VSF3_MONDO_13616 and tr_G3VUR7_G3VUR7_SARHA_9305 are exactly identical! WARNING: Sequences tr_U3KKR2_U3KKR2_FICAL_59894 and tr_A0A218UZT2_A0A218UZT2_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A2I3MLN7_A0A2I3MLN7_PAPAN_9555 and tr_A0A2K5MLU3_A0A2K5MLU3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I0LRQ7_A0A2I0LRQ7_COLLI_8932 and tr_A0A1V4JI28_A0A1V4JI28_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1S3M9S8_A0A1S3M9S8_SALSA_8030 and tr_A0A060W8P5_A0A060W8P5_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3S8K5_A0A1S3S8K5_SALSA_8030 and tr_A0A060WBG0_A0A060WBG0_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A2U3V0E6_A0A2U3V0E6_TURTR_9739 and tr_A0A2Y9M8F4_A0A2Y9M8F4_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3V0E6_A0A2U3V0E6_TURTR_9739 and tr_A0A2Y9SQ03_A0A2Y9SQ03_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3V0E6_A0A2U3V0E6_TURTR_9739 and tr_A0A384AUV4_A0A384AUV4_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U3V8D0_A0A2U3V8D0_TURTR_9739 and tr_A0A2Y9MVR4_A0A2Y9MVR4_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 32 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/Q96RK1/4_raxmlng_ancestral/Q96RK1.raxml.reduced.phy Alignment comprises 1 partitions and 184 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 184 Gaps: 22.77 % Invariant sites: 7.61 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RK1/4_raxmlng_ancestral/Q96RK1.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/Q96RK1/3_mltree/Q96RK1.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 46 / 3680 [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: -11919.180145 [00:00:00 -11919.180145] Initial branch length optimization [00:00:00 -11673.744294] Model parameter optimization (eps = 0.100000) [00:00:08] Tree #1, final logLikelihood: -11549.303882 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.321465,0.476062) (0.247942,1.251528) (0.147426,0.471741) (0.283166,1.649592) 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/Q96RK1/4_raxmlng_ancestral/Q96RK1.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RK1/4_raxmlng_ancestral/Q96RK1.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RK1/4_raxmlng_ancestral/Q96RK1.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q96RK1/4_raxmlng_ancestral/Q96RK1.raxml.log Analysis started: 12-Jul-2021 18:15:29 / finished: 12-Jul-2021 18:15:37 Elapsed time: 8.610 seconds Consumed energy: 0.755 Wh