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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 02-Jun-2021 18:18:56 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q06330/2_msa/Q06330_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q06330/3_mltree/Q06330.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q06330/4_raxmlng_ancestral/Q06330 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622647136 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/Q06330/2_msa/Q06330_nogap_msa.fasta [00:00:00] Loaded alignment with 591 taxa and 500 sites WARNING: Sequences tr_M3YZ51_M3YZ51_MUSPF_9669 and tr_A0A2Y9JLG1_A0A2Y9JLG1_ENHLU_391180 are exactly identical! WARNING: Sequences sp_P28159_SUH_DROME_7227 and tr_B4HXL8_B4HXL8_DROSE_7238 are exactly identical! WARNING: Sequences tr_B5DHG8_B5DHG8_DROPS_46245 and tr_B4GK80_B4GK80_DROPE_7234 are exactly identical! WARNING: Sequences tr_A0A2J8NVW7_A0A2J8NVW7_PANTR_9598 and sp_Q06330_SUH_HUMAN_9606 are exactly identical! WARNING: Sequences tr_U5PR56_U5PR56_SHEEP_9940 and tr_A0A2Y9S8T5_A0A2Y9S8T5_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A088A316_A0A088A316_APIME_7460 and tr_A0A0M9A9N2_A0A0M9A9N2_9HYME_166423 are exactly identical! WARNING: Sequences tr_A0A088A316_A0A088A316_APIME_7460 and tr_A0A0L7QXH1_A0A0L7QXH1_9HYME_597456 are exactly identical! WARNING: Sequences tr_A0A088A316_A0A088A316_APIME_7460 and tr_A0A2A3E9N9_A0A2A3E9N9_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A2I3LVJ8_A0A2I3LVJ8_PAPAN_9555 and tr_A0A2K5YEZ1_A0A2K5YEZ1_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0A1N7D6_A0A0A1N7D6_9FUNG_58291 and tr_A0A2G4T2T8_A0A2G4T2T8_9FUNG_1340429 are exactly identical! WARNING: Sequences tr_A0A0A1N7D6_A0A0A1N7D6_9FUNG_58291 and tr_A0A367JHB4_A0A367JHB4_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A151PA20_A0A151PA20_ALLMI_8496 and tr_A0A1U7SBE1_A0A1U7SBE1_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091EZX0_A0A091EZX0_CORBR_85066 and tr_A0A093QCJ7_A0A093QCJ7_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A091IQ83_A0A091IQ83_EGRGA_188379 and tr_A0A091X3X1_A0A091X3X1_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091IQ83_A0A091IQ83_EGRGA_188379 and tr_A0A087QNS2_A0A087QNS2_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091IQ83_A0A091IQ83_EGRGA_188379 and tr_A0A093HN58_A0A093HN58_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091IQ83_A0A091IQ83_EGRGA_188379 and tr_A0A0A0API3_A0A0A0API3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V0S5F6_A0A0V0S5F6_9BILA_6336 and tr_A0A0V0WN61_A0A0V0WN61_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1LCL7_A0A0V1LCL7_9BILA_6335 and tr_A0A0V0ZPD4_A0A0V0ZPD4_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V1LCL7_A0A0V1LCL7_9BILA_6335 and tr_A0A0V1P279_A0A0V1P279_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0XG07_A0A0V0XG07_TRIPS_6337 and tr_A0A0V0XG38_A0A0V0XG38_TRIPS_6337 are exactly identical! WARNING: Sequences tr_A0A0V1MSC0_A0A0V1MSC0_9BILA_268474 and tr_A0A0V1HYD4_A0A0V1HYD4_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A195DUS7_A0A195DUS7_9HYME_471704 and tr_A0A195EWU5_A0A195EWU5_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A195DUS7_A0A195DUS7_9HYME_471704 and tr_A0A195CB99_A0A195CB99_9HYME_456900 are exactly identical! WARNING: Sequences tr_A0A1R1WZ57_A0A1R1WZ57_9FUNG_133412 and tr_A0A1R1XHJ4_A0A1R1XHJ4_9FUNG_133412 are exactly identical! WARNING: Sequences tr_A0A1R1WZ57_A0A1R1WZ57_9FUNG_133412 and tr_A0A1R1XPU6_A0A1R1XPU6_9FUNG_133412 are exactly identical! WARNING: Sequences tr_A0A2H3DKW7_A0A2H3DKW7_ARMGA_47427 and tr_A0A2H3C5M3_A0A2H3C5M3_9AGAR_1076256 are exactly identical! WARNING: Sequences tr_A0A2H3DKW7_A0A2H3DKW7_ARMGA_47427 and tr_A0A284QM26_A0A284QM26_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2D0RWU5_A0A2D0RWU5_ICTPU_7998 and tr_A0A2D0RXH0_A0A2D0RXH0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2N5SQ87_A0A2N5SQ87_9BASI_200324 and tr_A0A2N5W112_A0A2N5W112_9BASI_200324 are exactly identical! WARNING: Duplicate sequences found: 30 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/Q06330/4_raxmlng_ancestral/Q06330.raxml.reduced.phy Alignment comprises 1 partitions and 500 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 500 Gaps: 18.69 % Invariant sites: 0.40 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q06330/4_raxmlng_ancestral/Q06330.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/Q06330/3_mltree/Q06330.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 125 / 10000 [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: -113466.494467 [00:00:00 -113466.494467] Initial branch length optimization [00:00:01 -109889.253758] Model parameter optimization (eps = 0.100000) [00:00:19] Tree #1, final logLikelihood: -109629.325569 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.194666,0.250452) (0.198940,0.384948) (0.312771,0.841744) (0.293624,2.082224) 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/Q06330/4_raxmlng_ancestral/Q06330.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q06330/4_raxmlng_ancestral/Q06330.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q06330/4_raxmlng_ancestral/Q06330.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q06330/4_raxmlng_ancestral/Q06330.raxml.log Analysis started: 02-Jun-2021 18:18:56 / finished: 02-Jun-2021 18:19:19 Elapsed time: 22.670 seconds Consumed energy: 1.474 Wh