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 18:36:20 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q7Z494/2_msa/Q7Z494_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q7Z494/3_mltree/Q7Z494.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q7Z494/4_raxmlng_ancestral/Q7Z494 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622648180 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/Q7Z494/2_msa/Q7Z494_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1330 sites WARNING: Sequences tr_B4QRQ9_B4QRQ9_DROSI_7240 and sp_P46824_KLC_DROME_7227 are exactly identical! WARNING: Sequences tr_E1BZD8_E1BZD8_CHICK_9031 and tr_A0A2I0MNL0_A0A2I0MNL0_COLLI_8932 are exactly identical! WARNING: Sequences tr_G3R2B3_G3R2B3_GORGO_9595 and tr_A0A2I3RWP0_A0A2I3RWP0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R2B3_G3R2B3_GORGO_9595 and tr_A0A2K5LRA8_A0A2K5LRA8_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3R2B3_G3R2B3_GORGO_9595 and tr_A0A2K6B8Q5_A0A2K6B8Q5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3R2B3_G3R2B3_GORGO_9595 and tr_A0A2R9B9F8_A0A2R9B9F8_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8P024_A0A2J8P024_PANTR_9598 and sp_Q9NSK0_KLC4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_F7HGT8_F7HGT8_MACMU_9544 and tr_A0A2K6E9A3_A0A2K6E9A3_MACNE_9545 are exactly identical! WARNING: Sequences tr_B3SAB7_B3SAB7_TRIAD_10228 and tr_A0A369S013_A0A369S013_9METZ_287889 are exactly identical! WARNING: Sequences tr_A0A093RV31_A0A093RV31_9PASS_328815 and tr_A0A091UL43_A0A091UL43_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A093RV31_A0A093RV31_9PASS_328815 and tr_A0A093GMA9_A0A093GMA9_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A091WB76_A0A091WB76_NIPNI_128390 and tr_A0A087R5B3_A0A087R5B3_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A087QQY0_A0A087QQY0_APTFO_9233 and tr_A0A091WHP7_A0A091WHP7_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A087QQY0_A0A087QQY0_APTFO_9233 and tr_A0A0A0A1B3_A0A0A0A1B3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A087QQY0_A0A087QQY0_APTFO_9233 and tr_A0A091HP51_A0A091HP51_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A093HMV4_A0A093HMV4_STRCA_441894 and tr_A0A099Z5D1_A0A099Z5D1_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A0V1CTC6_A0A0V1CTC6_TRIBR_45882 and tr_A0A0V1AC86_A0A0V1AC86_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0VQP4_A0A0V0VQP4_9BILA_181606 and tr_A0A0V0U242_A0A0V0U242_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S3SEM6_A0A1S3SEM6_SALSA_8030 and tr_A0A060WN40_A0A060WN40_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1D1V6Z3_A0A1D1V6Z3_RAMVA_947166 and tr_A0A1D1VEV5_A0A1D1VEV5_RAMVA_947166 are exactly identical! WARNING: Sequences tr_A0A2D0QKZ7_A0A2D0QKZ7_ICTPU_7998 and tr_A0A2D0QL01_A0A2D0QL01_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QKZ7_A0A2D0QKZ7_ICTPU_7998 and tr_A0A2D0QL83_A0A2D0QL83_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QKZ7_A0A2D0QKZ7_ICTPU_7998 and tr_A0A2D0QL87_A0A2D0QL87_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QKZ7_A0A2D0QKZ7_ICTPU_7998 and tr_A0A2D0QN45_A0A2D0QN45_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QKZ7_A0A2D0QKZ7_ICTPU_7998 and tr_A0A2D0QN50_A0A2D0QN50_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QKZ7_A0A2D0QKZ7_ICTPU_7998 and tr_A0A2D0QNY0_A0A2D0QNY0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QM80_A0A2D0QM80_ICTPU_7998 and tr_A0A2D0QQ71_A0A2D0QQ71_ICTPU_7998 are exactly identical! WARNING: Duplicate sequences found: 27 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/Q7Z494/4_raxmlng_ancestral/Q7Z494.raxml.reduced.phy Alignment comprises 1 partitions and 1330 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1330 Gaps: 58.76 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q7Z494/4_raxmlng_ancestral/Q7Z494.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/Q7Z494/3_mltree/Q7Z494.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 333 / 26640 [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: -419563.405774 [00:00:00 -419563.405774] Initial branch length optimization [00:00:03 -414194.590733] Model parameter optimization (eps = 0.100000) [00:01:12] Tree #1, final logLikelihood: -412826.871125 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.094014,0.491293) (0.046785,0.477610) (0.389427,0.688236) (0.469775,1.412271) 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/Q7Z494/4_raxmlng_ancestral/Q7Z494.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q7Z494/4_raxmlng_ancestral/Q7Z494.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q7Z494/4_raxmlng_ancestral/Q7Z494.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q7Z494/4_raxmlng_ancestral/Q7Z494.raxml.log Analysis started: 02-Jun-2021 18:36:20 / finished: 02-Jun-2021 18:37:43 Elapsed time: 83.633 seconds Consumed energy: 6.504 Wh