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 18:06:21 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N5M9/2_msa/Q8N5M9_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N5M9/3_mltree/Q8N5M9.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N5M9/4_raxmlng_ancestral/Q8N5M9 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626102381 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/Q8N5M9/2_msa/Q8N5M9_nogap_msa.fasta [00:00:00] Loaded alignment with 199 taxa and 183 sites WARNING: Sequences sp_Q5XKN4_JAGN1_MOUSE_10090 and sp_Q4KM64_JAGN1_RAT_10116 are exactly identical! WARNING: Sequences tr_G1QVZ4_G1QVZ4_NOMLE_61853 and tr_G3R3V7_G3R3V7_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1QVZ4_G1QVZ4_NOMLE_61853 and tr_H2QM11_H2QM11_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QVZ4_G1QVZ4_NOMLE_61853 and tr_G7MKR7_G7MKR7_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1QVZ4_G1QVZ4_NOMLE_61853 and tr_G8F652_G8F652_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1QVZ4_G1QVZ4_NOMLE_61853 and tr_A0A2I3LEM6_A0A2I3LEM6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1QVZ4_G1QVZ4_NOMLE_61853 and tr_A0A0D9RDJ8_A0A0D9RDJ8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1QVZ4_G1QVZ4_NOMLE_61853 and tr_A0A2K5LG24_A0A2K5LG24_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1QVZ4_G1QVZ4_NOMLE_61853 and tr_A0A2K6BJZ2_A0A2K6BJZ2_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1QVZ4_G1QVZ4_NOMLE_61853 and tr_A0A2K5ZXF1_A0A2K5ZXF1_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1QVZ4_G1QVZ4_NOMLE_61853 and tr_A0A2R9BJF1_A0A2R9BJF1_PANPA_9597 are exactly identical! WARNING: Sequences tr_J9NSD4_J9NSD4_CANLF_9615 and tr_D2HRA4_D2HRA4_AILME_9646 are exactly identical! WARNING: Sequences tr_J9NSD4_J9NSD4_CANLF_9615 and tr_A0A2U3VDQ5_A0A2U3VDQ5_ODORO_9708 are exactly identical! WARNING: Sequences tr_J9NSD4_J9NSD4_CANLF_9615 and tr_A0A2U3Y5R3_A0A2U3Y5R3_LEPWE_9713 are exactly identical! WARNING: Sequences tr_J9NSD4_J9NSD4_CANLF_9615 and tr_A0A2Y9J759_A0A2Y9J759_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A158NSP6_A0A158NSP6_ATTCE_12957 and tr_A0A151HYI8_A0A151HYI8_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A0K0JGC3_A0A0K0JGC3_BRUMA_6279 and tr_A0A0R3QAT7_A0A0R3QAT7_9BILA_42155 are exactly identical! WARNING: Sequences tr_E5SQZ0_E5SQZ0_TRISP_6334 and tr_A0A0V0S1X9_A0A0V0S1X9_9BILA_6336 are exactly identical! WARNING: Sequences tr_E5SQZ0_E5SQZ0_TRISP_6334 and tr_A0A0V1KQV6_A0A0V1KQV6_9BILA_6335 are exactly identical! WARNING: Sequences tr_E5SQZ0_E5SQZ0_TRISP_6334 and tr_A0A0V0ZUV0_A0A0V0ZUV0_9BILA_990121 are exactly identical! WARNING: Sequences tr_B3RY75_B3RY75_TRIAD_10228 and tr_A0A369SH70_A0A369SH70_9METZ_287889 are exactly identical! WARNING: Sequences tr_R1EDA4_R1EDA4_EMIHU_2903 and tr_R1F164_R1F164_EMIHU_2903 are exactly identical! WARNING: Sequences tr_A0A3B5XZ83_A0A3B5XZ83_WHEAT_4565 and tr_A0A3B5YWJ9_A0A3B5YWJ9_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A0V1DDA1_A0A0V1DDA1_TRIBR_45882 and tr_A0A0V0V304_A0A0V0V304_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1DDA1_A0A0V1DDA1_TRIBR_45882 and tr_A0A0V0TLP5_A0A0V0TLP5_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1MEP5_A0A0V1MEP5_9BILA_268474 and tr_A0A0V1HLZ3_A0A0V1HLZ3_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A1S3MU45_A0A1S3MU45_SALSA_8030 and tr_A0A060YLZ9_A0A060YLZ9_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A226NF89_A0A226NF89_CALSU_9009 and tr_A0A226PGL3_A0A226PGL3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U3UZD9_A0A2U3UZD9_TURTR_9739 and tr_A0A2Y9MHE6_A0A2Y9MHE6_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3UZD9_A0A2U3UZD9_TURTR_9739 and tr_A0A2Y9F3H0_A0A2Y9F3H0_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3UZD9_A0A2U3UZD9_TURTR_9739 and tr_A0A384AYX8_A0A384AYX8_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 31 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/Q8N5M9/4_raxmlng_ancestral/Q8N5M9.raxml.reduced.phy Alignment comprises 1 partitions and 183 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 183 Gaps: 6.07 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N5M9/4_raxmlng_ancestral/Q8N5M9.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/Q8N5M9/3_mltree/Q8N5M9.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 46 / 3680 [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: -17076.989946 [00:00:00 -17076.989946] Initial branch length optimization [00:00:00 -17059.290207] Model parameter optimization (eps = 0.100000) [00:00:05] Tree #1, final logLikelihood: -16846.017553 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.216507,0.793495) (0.302986,1.229106) (0.358152,0.836040) (0.122356,1.278011) 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/Q8N5M9/4_raxmlng_ancestral/Q8N5M9.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N5M9/4_raxmlng_ancestral/Q8N5M9.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N5M9/4_raxmlng_ancestral/Q8N5M9.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N5M9/4_raxmlng_ancestral/Q8N5M9.raxml.log Analysis started: 12-Jul-2021 18:06:21 / finished: 12-Jul-2021 18:06:27 Elapsed time: 5.954 seconds Consumed energy: 0.439 Wh