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 03-Jun-2021 01:48:59 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P35523/2_msa/P35523_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P35523/3_mltree/P35523.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P35523/4_raxmlng_ancestral/P35523 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622674139 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/P35523/2_msa/P35523_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 988 sites WARNING: Sequences tr_M3XTR6_M3XTR6_MUSPF_9669 and tr_A0A2Y9KKH4_A0A2Y9KKH4_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q9VGH7_CLCN2_DROME_7227 and tr_B4HHW9_B4HHW9_DROSE_7238 are exactly identical! WARNING: Sequences tr_G3R5V0_G3R5V0_GORGO_9595 and tr_H2PUW4_H2PUW4_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3R5V0_G3R5V0_GORGO_9595 and tr_K7BMC0_K7BMC0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R5V0_G3R5V0_GORGO_9595 and sp_P51793_CLCN4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R5V0_G3R5V0_GORGO_9595 and tr_F7BX81_F7BX81_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3R5V0_G3R5V0_GORGO_9595 and tr_A0A096NQK3_A0A096NQK3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3R5V0_G3R5V0_GORGO_9595 and tr_A0A0D9RRY3_A0A0D9RRY3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3R5V0_G3R5V0_GORGO_9595 and tr_A0A2K5P7H8_A0A2K5P7H8_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3R5V0_G3R5V0_GORGO_9595 and tr_A0A2K5XN49_A0A2K5XN49_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3R5V0_G3R5V0_GORGO_9595 and tr_A0A2R8Z8M5_A0A2R8Z8M5_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q5RBK4_CLCN5_PONAB_9601 and sp_P51795_CLCN5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F1PWQ5_F1PWQ5_CANLF_9615 and tr_A0A2U3WKA5_A0A2U3WKA5_ODORO_9708 are exactly identical! WARNING: Sequences tr_H2QVJ5_H2QVJ5_PANTR_9598 and tr_A0A2R8ZSS9_A0A2R8ZSS9_PANPA_9597 are exactly identical! WARNING: Sequences tr_K7B9J0_K7B9J0_PANTR_9598 and tr_A0A2R9AD48_A0A2R9AD48_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6ZVD4_F6ZVD4_MONDO_13616 and tr_G3WSV4_G3WSV4_SARHA_9305 are exactly identical! WARNING: Sequences tr_W5PKM0_W5PKM0_SHEEP_9940 and tr_Q4F894_Q4F894_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A158P2X7_A0A158P2X7_ATTCE_12957 and tr_A0A195BPF1_A0A195BPF1_9HYME_520822 are exactly identical! WARNING: Sequences tr_F6QD86_F6QD86_MACMU_9544 and tr_G7NYZ6_G7NYZ6_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6QD86_F6QD86_MACMU_9544 and tr_A0A2I3M671_A0A2I3M671_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6QD86_F6QD86_MACMU_9544 and tr_A0A2K5N3F2_A0A2K5N3F2_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6QD86_F6QD86_MACMU_9544 and tr_A0A2K6BR48_A0A2K6BR48_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6V6U2_F6V6U2_MACMU_9544 and tr_G7Q2R0_G7Q2R0_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6V6U2_F6V6U2_MACMU_9544 and tr_A0A096MKP6_A0A096MKP6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6V6U2_F6V6U2_MACMU_9544 and tr_A0A0D9RK29_A0A0D9RK29_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6V6U2_F6V6U2_MACMU_9544 and tr_A0A2K5M2N3_A0A2K5M2N3_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6V6U2_F6V6U2_MACMU_9544 and tr_A0A2K6E3J7_A0A2K6E3J7_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6V6U2_F6V6U2_MACMU_9544 and tr_A0A2K5XEP2_A0A2K5XEP2_MANLE_9568 are exactly identical! WARNING: Sequences tr_F4WZJ2_F4WZJ2_ACREC_103372 and tr_A0A195DRD7_A0A195DRD7_9HYME_471704 are exactly identical! WARNING: Sequences tr_F4WZJ2_F4WZJ2_ACREC_103372 and tr_A0A195ET15_A0A195ET15_9HYME_34720 are exactly identical! WARNING: Sequences tr_G1M083_G1M083_AILME_9646 and tr_A0A384C1S5_A0A384C1S5_URSMA_29073 are exactly identical! WARNING: Sequences tr_G7Q273_G7Q273_MACFA_9541 and tr_A0A2K6DC20_A0A2K6DC20_MACNE_9545 are exactly identical! WARNING: Sequences tr_W2QC05_W2QC05_PHYPN_761204 and tr_W2L9W3_W2L9W3_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A151P7H2_A0A151P7H2_ALLMI_8496 and tr_A0A1U7SIC8_A0A1U7SIC8_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A165A4N9_A0A165A4N9_9HOMO_1314777 and tr_A0A166IBW7_A0A166IBW7_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A2D0T1R0_A0A2D0T1R0_ICTPU_7998 and tr_W5UD41_W5UD41_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4C162_A0A2U4C162_TURTR_9739 and tr_A0A2Y9MB75_A0A2Y9MB75_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 37 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/P35523/4_raxmlng_ancestral/P35523.raxml.reduced.phy Alignment comprises 1 partitions and 988 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 988 Gaps: 33.89 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P35523/4_raxmlng_ancestral/P35523.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/P35523/3_mltree/P35523.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 247 / 19760 [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: -352910.928909 [00:00:00 -352910.928909] Initial branch length optimization [00:00:01 -351457.885539] Model parameter optimization (eps = 0.100000) [00:01:02] Tree #1, final logLikelihood: -350067.022229 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.165294,0.334410) (0.159941,0.366900) (0.321053,0.773560) (0.353713,1.802841) 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/P35523/4_raxmlng_ancestral/P35523.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P35523/4_raxmlng_ancestral/P35523.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P35523/4_raxmlng_ancestral/P35523.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P35523/4_raxmlng_ancestral/P35523.raxml.log Analysis started: 03-Jun-2021 01:48:59 / finished: 03-Jun-2021 01:50:12 Elapsed time: 72.212 seconds Consumed energy: 5.651 Wh