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 17:56:22 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13308/2_msa/Q13308_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13308/3_mltree/Q13308.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13308/4_raxmlng_ancestral/Q13308 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622645782 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/Q13308/2_msa/Q13308_nogap_msa.fasta [00:00:00] Loaded alignment with 1000 taxa and 1070 sites WARNING: Sequences tr_A0A2R8Q165_A0A2R8Q165_DANRE_7955 and tr_A0A2R8QG87_A0A2R8QG87_DANRE_7955 are exactly identical! WARNING: Sequences tr_M3XXA3_M3XXA3_MUSPF_9669 and tr_A0A2Y9JTT4_A0A2Y9JTT4_ENHLU_391180 are exactly identical! WARNING: Sequences tr_H2PSJ2_H2PSJ2_PONAB_9601 and tr_A0A2J8MRU2_A0A2J8MRU2_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2PSJ2_H2PSJ2_PONAB_9601 and tr_A0A2R9BIL6_A0A2R9BIL6_PANPA_9597 are exactly identical! WARNING: Sequences tr_Q28WN9_Q28WN9_DROPS_46245 and tr_B4H763_B4H763_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A2I3SW69_A0A2I3SW69_PANTR_9598 and tr_A0A2R9C2C0_A0A2R9C2C0_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3TDX1_A0A2I3TDX1_PANTR_9598 and tr_A0A2R9BV68_A0A2R9BV68_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7DGW1_F7DGW1_MACMU_9544 and tr_G7PSM1_G7PSM1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7DGW1_F7DGW1_MACMU_9544 and tr_A0A2I3MH64_A0A2I3MH64_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7DGW1_F7DGW1_MACMU_9544 and tr_A0A2K6BIB6_A0A2K6BIB6_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0ZEE4_H0ZEE4_TAEGU_59729 and tr_A0A218V095_A0A218V095_9PASE_299123 are exactly identical! WARNING: Sequences tr_G7PLY7_G7PLY7_MACFA_9541 and tr_A0A2K6DPF9_A0A2K6DPF9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A091J1T1_A0A091J1T1_EGRGA_188379 and tr_A0A087RHY4_A0A087RHY4_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091J1T1_A0A091J1T1_EGRGA_188379 and tr_A0A091H7N1_A0A091H7N1_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091JI37_A0A091JI37_EGRGA_188379 and tr_A0A091WR17_A0A091WR17_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JI37_A0A091JI37_EGRGA_188379 and tr_A0A087RDZ5_A0A087RDZ5_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091VGU9_A0A091VGU9_NIPNI_128390 and tr_A0A087R5C7_A0A087R5C7_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A0V1CN21_A0A0V1CN21_TRIBR_45882 and tr_A0A0V0UA62_A0A0V0UA62_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1CTU0_A0A0V1CTU0_TRIBR_45882 and tr_A0A0V0VPJ4_A0A0V0VPJ4_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CTU0_A0A0V1CTU0_TRIBR_45882 and tr_A0A0V0U2C7_A0A0V0U2C7_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0WJD9_A0A0V0WJD9_9BILA_92179 and tr_A0A0V1L8K5_A0A0V1L8K5_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0WJD9_A0A0V0WJD9_9BILA_92179 and tr_A0A0V1PMA2_A0A0V1PMA2_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0X2J3_A0A0V0X2J3_9BILA_92179 and tr_A0A0V1L3W9_A0A0V1L3W9_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1MY60_A0A0V1MY60_9BILA_268474 and tr_A0A0V1MYP3_A0A0V1MYP3_9BILA_268474 are exactly identical! WARNING: Sequences tr_A0A2D0RQ96_A0A2D0RQ96_ICTPU_7998 and tr_A0A2D0RQA0_A0A2D0RQA0_ICTPU_7998 are exactly identical! WARNING: Duplicate sequences found: 25 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/Q13308/4_raxmlng_ancestral/Q13308.raxml.reduced.phy Alignment comprises 1 partitions and 1070 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1070 Gaps: 43.86 % Invariant sites: 0.37 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13308/4_raxmlng_ancestral/Q13308.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/Q13308/3_mltree/Q13308.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 268 / 21440 [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: -341926.694847 [00:00:00 -341926.694847] Initial branch length optimization [00:00:04 -332420.160675] Model parameter optimization (eps = 0.100000) [00:02:21] Tree #1, final logLikelihood: -331262.896091 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.100515,0.259952) (0.098639,0.333584) (0.421159,0.856811) (0.379687,1.527870) 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/Q13308/4_raxmlng_ancestral/Q13308.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13308/4_raxmlng_ancestral/Q13308.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13308/4_raxmlng_ancestral/Q13308.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q13308/4_raxmlng_ancestral/Q13308.raxml.log Analysis started: 02-Jun-2021 17:56:22 / finished: 02-Jun-2021 17:58:55 Elapsed time: 152.646 seconds Consumed energy: 7.038 Wh