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 12-Jul-2021 17:48:12 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P15814/2_msa/P15814_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P15814/3_mltree/P15814.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P15814/4_raxmlng_ancestral/P15814 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626101292 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/P15814/2_msa/P15814_nogap_msa.fasta [00:00:00] Loaded alignment with 865 taxa and 213 sites WARNING: Sequences tr_A0A075B5J3_A0A075B5J3_MOUSE_10090 and tr_A0A075B5J4_A0A075B5J4_MOUSE_10090 are exactly identical! WARNING: Sequences tr_A0A0G2JE99_A0A0G2JE99_MOUSE_10090 and sp_P01843_LAC1_MOUSE_10090 are exactly identical! WARNING: Sequences sp_P01851_TCB2_MOUSE_10090 and sp_P01852_TCB1_MOUSE_10090 are exactly identical! WARNING: Sequences tr_A0A3B3HDM6_A0A3B3HDM6_ORYLA_8090 and tr_H2L5S7_H2L5S7_ORYLA_8090 are exactly identical! WARNING: Sequences tr_G1PV74_G1PV74_MYOLU_59463 and tr_G1PY90_G1PY90_MYOLU_59463 are exactly identical! WARNING: Sequences tr_A0A2I2Y8M1_A0A2I2Y8M1_GORGO_9595 and tr_A0A2R9AKE6_A0A2R9AKE6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2YH49_A0A2I2YH49_GORGO_9595 and tr_A0A2I3RH44_A0A2I3RH44_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2ZX49_A0A2I2ZX49_GORGO_9595 and tr_A0A2R8ZL01_A0A2R8ZL01_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3SEV9_G3SEV9_GORGO_9595 and tr_H2RGZ2_H2RGZ2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SEV9_G3SEV9_GORGO_9595 and tr_A0A2R8ZIP7_A0A2R8ZIP7_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2PIP9_H2PIP9_PONAB_9601 and sp_P06340_DOA_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P03988_IGHM_RABIT_9986 and sp_P04221_MUCM_RABIT_9986 are exactly identical! WARNING: Sequences tr_A0A2I3RU10_A0A2I3RU10_PANTR_9598 and tr_A0A2R9AJV4_A0A2R9AJV4_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QSR5_H2QSR5_PANTR_9598 and tr_A0A2R9BJY2_A0A2R9BJY2_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QSS4_H2QSS4_PANTR_9598 and tr_A0A2R9AKD7_A0A2R9AKD7_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A3B5PWQ2_A0A3B5PWQ2_XIPMA_8083 and tr_A0A3B5R2P9_A0A3B5R2P9_XIPMA_8083 are exactly identical! WARNING: Sequences tr_A0A3B5QJB4_A0A3B5QJB4_XIPMA_8083 and tr_A0A3B5RCG4_A0A3B5RCG4_XIPMA_8083 are exactly identical! WARNING: Sequences tr_F6QQP0_F6QQP0_MACMU_9544 and tr_A0A2I3NC97_A0A2I3NC97_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6QQP0_F6QQP0_MACMU_9544 and tr_A0A2K5NW12_A0A2K5NW12_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6QQP0_F6QQP0_MACMU_9544 and tr_A0A2K6AZT5_A0A2K6AZT5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6QQP0_F6QQP0_MACMU_9544 and tr_A0A2K5XM92_A0A2K5XM92_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3P3W4_G3P3W4_GASAC_69293 and tr_G3Q4B0_G3Q4B0_GASAC_69293 are exactly identical! WARNING: Sequences tr_A0A2I3LVY2_A0A2I3LVY2_PAPAN_9555 and tr_A0A2I3MA75_A0A2I3MA75_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3LVY2_A0A2I3LVY2_PAPAN_9555 and tr_A0A2K5KN32_A0A2K5KN32_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3LVY2_A0A2I3LVY2_PAPAN_9555 and tr_A0A2K5KNX6_A0A2K5KNX6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3LVY2_A0A2I3LVY2_PAPAN_9555 and tr_A0A2K6AZI7_A0A2K6AZI7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3LVY2_A0A2I3LVY2_PAPAN_9555 and tr_A0A2K5XMN1_A0A2K5XMN1_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3LVY2_A0A2I3LVY2_PAPAN_9555 and tr_A0A2K5XW74_A0A2K5XW74_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3MCZ4_A0A2I3MCZ4_PAPAN_9555 and tr_A0A2K6AWE3_A0A2K6AWE3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3MCZ4_A0A2I3MCZ4_PAPAN_9555 and tr_A0A2K5XR48_A0A2K5XR48_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3MI51_A0A2I3MI51_PAPAN_9555 and tr_A0A2K5ZHG0_A0A2K5ZHG0_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5NSF3_A0A2K5NSF3_CERAT_9531 and tr_A0A2K5XNN4_A0A2K5XNN4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5NVH7_A0A2K5NVH7_CERAT_9531 and tr_A0A2K6AWZ7_A0A2K6AWZ7_MACNE_9545 are exactly identical! WARNING: Duplicate sequences found: 33 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/P15814/4_raxmlng_ancestral/P15814.raxml.reduced.phy Alignment comprises 1 partitions and 213 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 213 Gaps: 38.92 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P15814/4_raxmlng_ancestral/P15814.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/P15814/3_mltree/P15814.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 54 / 4320 [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: -94795.102779 [00:00:00 -94795.102779] Initial branch length optimization [00:00:00 -87005.795530] Model parameter optimization (eps = 0.100000) [00:00:29] Tree #1, final logLikelihood: -86744.991135 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.074533,0.346787) (0.070677,0.346914) (0.391336,0.813741) (0.463454,1.361922) 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/P15814/4_raxmlng_ancestral/P15814.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P15814/4_raxmlng_ancestral/P15814.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P15814/4_raxmlng_ancestral/P15814.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P15814/4_raxmlng_ancestral/P15814.raxml.log Analysis started: 12-Jul-2021 17:48:12 / finished: 12-Jul-2021 17:48:43 Elapsed time: 31.114 seconds Consumed energy: 2.322 Wh