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 17:47:43 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A0A087WSX0/2_msa/A0A087WSX0_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A0A087WSX0/3_mltree/A0A087WSX0.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A0A087WSX0/4_raxmlng_ancestral/A0A087WSX0 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626101263 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/A0A087WSX0/2_msa/A0A087WSX0_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 123 sites WARNING: Sequences sp_P04210_LV1_CHICK_9031 and tr_R9PXM5_R9PXM5_CHICK_9031 are exactly identical! WARNING: Sequences tr_A0A2I2YJC5_A0A2I2YJC5_GORGO_9595 and tr_A0A2I3RV96_A0A2I3RV96_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RK08_G3RK08_GORGO_9595 and tr_A0A2I3S3B0_A0A2I3S3B0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RK08_G3RK08_GORGO_9595 and sp_P12018_VPREB_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RK08_G3RK08_GORGO_9595 and tr_A0A2R9BNT9_A0A2R9BNT9_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3SDJ0_G3SDJ0_GORGO_9595 and tr_H2QLC7_H2QLC7_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2P3Q5_H2P3Q5_PONAB_9601 and tr_F7DFA6_F7DFA6_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2P3Q5_H2P3Q5_PONAB_9601 and tr_G8F424_G8F424_MACFA_9541 are exactly identical! WARNING: Sequences tr_H2P3Q5_H2P3Q5_PONAB_9601 and tr_A0A0D9RMS9_A0A0D9RMS9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_J9P8P3_J9P8P3_CANLF_9615 and tr_J9PAD4_J9PAD4_CANLF_9615 are exactly identical! WARNING: Sequences tr_A0A2I3SR69_A0A2I3SR69_PANTR_9598 and tr_A0A2R8ZB48_A0A2R8ZB48_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3T0N1_A0A2I3T0N1_PANTR_9598 and tr_A0A2R8ZDA9_A0A2R8ZDA9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3TQF9_A0A2I3TQF9_PANTR_9598 and tr_A0A2R8ZQY1_A0A2R8ZQY1_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3TUR2_A0A2I3TUR2_PANTR_9598 and tr_A0A2R8ZX92_A0A2R8ZX92_PANPA_9597 are exactly identical! WARNING: Sequences sp_A0A0B4J1Y8_LV949_HUMAN_9606 and tr_A0A2R9A2R6_A0A2R9A2R6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5QR47_A0A1D5QR47_MACMU_9544 and tr_G8F2W8_G8F2W8_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6SWU6_F6SWU6_MACMU_9544 and tr_G8F5L7_G8F5L7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7F215_F7F215_MACMU_9544 and tr_A0A2K6ARQ7_A0A2K6ARQ7_MACNE_9545 are exactly identical! WARNING: Sequences tr_G8F1D9_G8F1D9_MACMU_9544 and tr_G8F609_G8F609_MACFA_9541 are exactly identical! WARNING: Sequences tr_G8F1D9_G8F1D9_MACMU_9544 and tr_A0A0D9RG94_A0A0D9RG94_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G8F1D9_G8F1D9_MACMU_9544 and tr_A0A2K5M4Y2_A0A2K5M4Y2_CERAT_9531 are exactly identical! WARNING: Sequences tr_G8F1D9_G8F1D9_MACMU_9544 and tr_A0A2K6BRF2_A0A2K6BRF2_MACNE_9545 are exactly identical! WARNING: Sequences tr_G8F1D9_G8F1D9_MACMU_9544 and tr_A0A2K5Y552_A0A2K5Y552_MANLE_9568 are exactly identical! WARNING: Sequences tr_H9H4S2_H9H4S2_MACMU_9544 and tr_H9H5B4_H9H5B4_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2R8MJT0_A0A2R8MJT0_CALJA_9483 and tr_A0A2R8P774_A0A2R8P774_CALJA_9483 are exactly identical! WARNING: Sequences tr_G7PHB9_G7PHB9_MACFA_9541 and tr_A0A096NSB1_A0A096NSB1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7PHB9_G7PHB9_MACFA_9541 and tr_A0A2K5XPA3_A0A2K5XPA3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0D9RN59_A0A0D9RN59_CHLSB_60711 and tr_A0A0D9RN85_A0A0D9RN85_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2K5KMJ7_A0A2K5KMJ7_CERAT_9531 and tr_A0A2K5XYB4_A0A2K5XYB4_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 29 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/A0A087WSX0/4_raxmlng_ancestral/A0A087WSX0.raxml.reduced.phy Alignment comprises 1 partitions and 123 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 123 Gaps: 11.52 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A0A087WSX0/4_raxmlng_ancestral/A0A087WSX0.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/A0A087WSX0/3_mltree/A0A087WSX0.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 31 / 2480 [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: -58636.608324 [00:00:00 -58636.608324] Initial branch length optimization [00:00:00 -58329.452111] Model parameter optimization (eps = 0.100000) [00:00:15] Tree #1, final logLikelihood: -58090.401592 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.189349,0.391550) (0.136094,0.419411) (0.481757,0.914070) (0.192800,2.222104) 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/A0A087WSX0/4_raxmlng_ancestral/A0A087WSX0.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A0A087WSX0/4_raxmlng_ancestral/A0A087WSX0.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A0A087WSX0/4_raxmlng_ancestral/A0A087WSX0.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A0A087WSX0/4_raxmlng_ancestral/A0A087WSX0.raxml.log Analysis started: 12-Jul-2021 17:47:43 / finished: 12-Jul-2021 17:48:00 Elapsed time: 16.578 seconds Consumed energy: 1.411 Wh