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 02-Jun-2021 18:25:28 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P07320/2_msa/P07320_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P07320/3_mltree/P07320.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P07320/4_raxmlng_ancestral/P07320 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622647528 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/P07320/2_msa/P07320_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 174 sites WARNING: Sequences tr_M3YC57_M3YC57_MUSPF_9669 and tr_A0A2Y9K901_A0A2Y9K901_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G3RCE9_G3RCE9_GORGO_9595 and sp_P22914_CRYGS_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RMA8_G3RMA8_GORGO_9595 and tr_H2QJB0_H2QJB0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RMA8_G3RMA8_GORGO_9595 and sp_P07320_CRGD_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RUZ8_G3RUZ8_GORGO_9595 and tr_H2QJB1_H2QJB1_PANTR_9598 are exactly identical! WARNING: Sequences tr_A7KK31_A7KK31_PANTR_9598 and sp_P11844_CRGA_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A7KK31_A7KK31_PANTR_9598 and tr_A7KK28_A7KK28_PANPA_9597 are exactly identical! WARNING: Sequences sp_A3RLD8_CRGC_MACMU_9544 and tr_G7PLA8_G7PLA8_MACFA_9541 are exactly identical! WARNING: Sequences tr_A7KK27_A7KK27_MACMU_9544 and tr_A0A2I3N8B8_A0A2I3N8B8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A7KK27_A7KK27_MACMU_9544 and tr_A0A2K5NYX4_A0A2K5NYX4_CERAT_9531 are exactly identical! WARNING: Sequences tr_A7KK27_A7KK27_MACMU_9544 and tr_A0A2K6A4K3_A0A2K6A4K3_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6WSD9_F6WSD9_MACMU_9544 and tr_G7NYM3_G7NYM3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6WSD9_F6WSD9_MACMU_9544 and tr_A0A096NCK3_A0A096NCK3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6WSD9_F6WSD9_MACMU_9544 and tr_A0A0D9RNN2_A0A0D9RNN2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6WSD9_F6WSD9_MACMU_9544 and tr_A0A2K5P3E0_A0A2K5P3E0_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6WSD9_F6WSD9_MACMU_9544 and tr_A0A2K6C2J9_A0A2K6C2J9_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6WSD9_F6WSD9_MACMU_9544 and tr_A0A2K5XZH8_A0A2K5XZH8_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7AV55_F7AV55_MACMU_9544 and tr_G7PLA7_G7PLA7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7AV55_F7AV55_MACMU_9544 and tr_A0A2I3MTV9_A0A2I3MTV9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7AV55_F7AV55_MACMU_9544 and tr_A0A2K5MVY4_A0A2K5MVY4_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7AV55_F7AV55_MACMU_9544 and tr_A0A2K5XTU2_A0A2K5XTU2_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7PLA9_G7PLA9_MACFA_9541 and tr_A0A0D9RCE9_A0A0D9RCE9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3MKU1_A0A2I3MKU1_PAPAN_9555 and tr_A0A2K5MMW1_A0A2K5MMW1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MRW5_A0A2I3MRW5_PAPAN_9555 and tr_A0A2K5MJV9_A0A2K5MJV9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MRW5_A0A2I3MRW5_PAPAN_9555 and tr_A0A2K6B305_A0A2K6B305_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3MRW5_A0A2I3MRW5_PAPAN_9555 and tr_A0A2K6AKB7_A0A2K6AKB7_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A1S3MZ73_A0A1S3MZ73_SALSA_8030 and tr_A0A060YHG4_A0A060YHG4_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3PN29_A0A1S3PN29_SALSA_8030 and tr_A0A060WPA1_A0A060WPA1_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3R9S1_A0A1S3R9S1_SALSA_8030 and tr_A0A060W811_A0A060W811_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1L8HNK9_A0A1L8HNK9_XENLA_8355 and tr_A0A1L8HNL8_A0A1L8HNL8_XENLA_8355 are exactly identical! WARNING: Sequences tr_A0A2D0QDS0_A0A2D0QDS0_ICTPU_7998 and tr_A0A2D0QFT5_A0A2D0QFT5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QGD4_A0A2D0QGD4_ICTPU_7998 and tr_A0A2D0QGD9_A0A2D0QGD9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5N1A1_A0A2K5N1A1_CERAT_9531 and tr_A0A2K5XZP1_A0A2K5XZP1_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U3WVG0_A0A2U3WVG0_ODORO_9708 and tr_A0A2U3YHV0_A0A2U3YHV0_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 34 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/P07320/4_raxmlng_ancestral/P07320.raxml.reduced.phy Alignment comprises 1 partitions and 174 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 174 Gaps: 2.65 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P07320/4_raxmlng_ancestral/P07320.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/P07320/3_mltree/P07320.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 44 / 3520 [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: -64729.230763 [00:00:00 -64729.230763] Initial branch length optimization [00:00:00 -63870.620978] Model parameter optimization (eps = 0.100000) [00:00:23] Tree #1, final logLikelihood: -63537.843013 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.221795,0.408894) (0.200769,0.637717) (0.416377,1.071630) (0.161060,2.080432) 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/P07320/4_raxmlng_ancestral/P07320.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P07320/4_raxmlng_ancestral/P07320.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P07320/4_raxmlng_ancestral/P07320.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P07320/4_raxmlng_ancestral/P07320.raxml.log Analysis started: 02-Jun-2021 18:25:28 / finished: 02-Jun-2021 18:25:53 Elapsed time: 25.230 seconds Consumed energy: 2.082 Wh