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 02-Jun-2021 18:32:25 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q16236/2_msa/Q16236_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q16236/3_mltree/Q16236.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q16236/4_raxmlng_ancestral/Q16236 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622647945 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/Q16236/2_msa/Q16236_nogap_msa.fasta [00:00:00] Loaded alignment with 664 taxa and 605 sites WARNING: Sequences tr_E9GNG2_E9GNG2_DAPPU_6669 and tr_E9I1S1_E9I1S1_DAPPU_6669 are exactly identical! WARNING: Sequences tr_E1BZR5_E1BZR5_CHICK_9031 and tr_G1NLK3_G1NLK3_MELGA_9103 are exactly identical! WARNING: Sequences tr_E1BZR5_E1BZR5_CHICK_9031 and tr_A0A087R740_A0A087R740_APTFO_9233 are exactly identical! WARNING: Sequences tr_E1BZR5_E1BZR5_CHICK_9031 and tr_A0A0A0AN41_A0A0A0AN41_CHAVO_50402 are exactly identical! WARNING: Sequences tr_G1RSC0_G1RSC0_NOMLE_61853 and tr_G3R9U1_G3R9U1_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RSC0_G1RSC0_NOMLE_61853 and sp_Q9BYV9_BACH2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RSC0_G1RSC0_NOMLE_61853 and tr_A0A2R9AEE7_A0A2R9AEE7_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QKL6_G3QKL6_GORGO_9595 and sp_Q16621_NFE2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8Q0U0_A0A2J8Q0U0_PANTR_9598 and tr_A0A2R8ZQP3_A0A2R8ZQP3_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QKW7_H2QKW7_PANTR_9598 and tr_A0A2R9A2Q5_A0A2R9A2Q5_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R463_H2R463_PANTR_9598 and sp_Q14494_NF2L1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2R463_H2R463_PANTR_9598 and tr_A0A2R9ANQ5_A0A2R9ANQ5_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6QF08_F6QF08_MACMU_9544 and tr_A0A2K6DI56_A0A2K6DI56_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6T3Z4_F6T3Z4_MACMU_9544 and tr_G7PU65_G7PU65_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6T3Z4_F6T3Z4_MACMU_9544 and tr_A0A2I3LVC0_A0A2I3LVC0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6T3Z4_F6T3Z4_MACMU_9544 and tr_A0A0D9S3Q4_A0A0D9S3Q4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6T3Z4_F6T3Z4_MACMU_9544 and tr_A0A2K5NEA9_A0A2K5NEA9_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6T3Z4_F6T3Z4_MACMU_9544 and tr_A0A2K6CZD4_A0A2K6CZD4_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6T3Z4_F6T3Z4_MACMU_9544 and tr_A0A2K5ZR84_A0A2K5ZR84_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6ZW90_F6ZW90_MACMU_9544 and tr_G7P420_G7P420_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6ZW90_F6ZW90_MACMU_9544 and tr_A0A096NRN0_A0A096NRN0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6ZW90_F6ZW90_MACMU_9544 and tr_A0A2K5MR12_A0A2K5MR12_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6ZW90_F6ZW90_MACMU_9544 and tr_A0A2K6ADP7_A0A2K6ADP7_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7ELK8_F7ELK8_MACMU_9544 and tr_G7P1L7_G7P1L7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7ELK8_F7ELK8_MACMU_9544 and tr_A0A2K5Z2H9_A0A2K5Z2H9_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7H4R2_F7H4R2_MACMU_9544 and tr_G8F5B9_G8F5B9_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7H4R2_F7H4R2_MACMU_9544 and tr_A0A2K5NQT5_A0A2K5NQT5_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A091W1J4_A0A091W1J4_NIPNI_128390 and tr_A0A093G7J5_A0A093G7J5_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A226MKU7_A0A226MKU7_CALSU_9009 and tr_A0A226P2C5_A0A226P2C5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0SRH9_A0A2D0SRH9_ICTPU_7998 and tr_A0A2D0SS25_A0A2D0SS25_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4AHP7_A0A2U4AHP7_TURTR_9739 and tr_A0A2Y9EWR8_A0A2Y9EWR8_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 31 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/Q16236/4_raxmlng_ancestral/Q16236.raxml.reduced.phy Alignment comprises 1 partitions and 605 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 605 Gaps: 31.10 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q16236/4_raxmlng_ancestral/Q16236.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/Q16236/3_mltree/Q16236.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 152 / 12160 [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: -158645.961067 [00:00:00 -158645.961067] Initial branch length optimization [00:00:01 -157158.545010] Model parameter optimization (eps = 0.100000) [00:00:33] Tree #1, final logLikelihood: -156734.489212 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.093776,0.400456) (0.043411,0.238097) (0.334053,0.659278) (0.528760,1.384138) 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/Q16236/4_raxmlng_ancestral/Q16236.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q16236/4_raxmlng_ancestral/Q16236.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q16236/4_raxmlng_ancestral/Q16236.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q16236/4_raxmlng_ancestral/Q16236.raxml.log Analysis started: 02-Jun-2021 18:32:25 / finished: 02-Jun-2021 18:33:03 Elapsed time: 37.638 seconds Consumed energy: 2.053 Wh