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 18:22:04 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6AWC2/2_msa/Q6AWC2_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6AWC2/3_mltree/Q6AWC2.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6AWC2/4_raxmlng_ancestral/Q6AWC2 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626103324 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/Q6AWC2/2_msa/Q6AWC2_nogap_msa.fasta [00:00:00] Loaded alignment with 999 taxa and 1192 sites WARNING: Sequences tr_B4QFM5_B4QFM5_DROSI_7240 and tr_B4I7K2_B4I7K2_DROSE_7238 are exactly identical! WARNING: Sequences tr_J3K9N9_J3K9N9_COCIM_246410 and tr_E9CRR5_E9CRR5_COCPS_443226 are exactly identical! WARNING: Sequences tr_J3K9N9_J3K9N9_COCIM_246410 and tr_A0A0J6YB63_A0A0J6YB63_COCIT_404692 are exactly identical! WARNING: Sequences tr_G3QG32_G3QG32_GORGO_9595 and tr_H2QUU4_H2QUU4_PANTR_9598 are exactly identical! WARNING: Sequences tr_C0NMQ2_C0NMQ2_AJECG_447093 and tr_C6H2E0_C6H2E0_AJECH_544712 are exactly identical! WARNING: Sequences tr_C0NMQ2_C0NMQ2_AJECG_447093 and tr_F0U541_F0U541_AJEC8_544711 are exactly identical! WARNING: Sequences tr_A0A179UHY6_A0A179UHY6_BLAGS_559298 and tr_C5GFJ5_C5GFJ5_AJEDR_559297 are exactly identical! WARNING: Sequences tr_A0A1D5QV36_A0A1D5QV36_MACMU_9544 and tr_A0A2K6DEX0_A0A2K6DEX0_MACNE_9545 are exactly identical! WARNING: Sequences tr_F9XPD8_F9XPD8_ZYMTI_336722 and tr_A0A1X7S762_A0A1X7S762_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G0MM60_G0MM60_CAEBE_135651 and tr_G0NV82_G0NV82_CAEBE_135651 are exactly identical! WARNING: Sequences tr_A8WZ81_A8WZ81_CAEBR_6238 and tr_A0A2G5VT08_A0A2G5VT08_9PELO_1611254 are exactly identical! WARNING: Sequences tr_M2Z2Z1_M2Z2Z1_PSEFD_383855 and tr_A0A139HWE0_A0A139HWE0_9PEZI_321146 are exactly identical! WARNING: Sequences tr_V2WZL5_V2WZL5_MONRO_1381753 and tr_A0A0W0F231_A0A0W0F231_9AGAR_221103 are exactly identical! WARNING: Sequences tr_V2X9P0_V2X9P0_MONRO_1381753 and tr_A0A0W0G149_A0A0W0G149_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A0L0RZ82_A0A0L0RZ82_ALLMA_578462 and tr_A0A0L0S7E5_A0A0L0S7E5_ALLMA_578462 are exactly identical! WARNING: Sequences tr_A0A1B7N8Y7_A0A1B7N8Y7_9HOMO_1314800 and tr_A0A1J8PMS3_A0A1J8PMS3_9HOMO_180088 are exactly identical! WARNING: Sequences tr_A0A1I7UEW2_A0A1I7UEW2_9PELO_1561998 and tr_A0A1I7UEW3_A0A1I7UEW3_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A2H3DN70_A0A2H3DN70_ARMGA_47427 and tr_A0A2H3C4G0_A0A2H3C4G0_9AGAR_1076256 are exactly identical! WARNING: Sequences tr_A0A2H3DN70_A0A2H3DN70_ARMGA_47427 and tr_A0A284QUR2_A0A284QUR2_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2H3BZE7_A0A2H3BZE7_9AGAR_1076256 and tr_A0A284RFW1_A0A284RFW1_9AGAR_47428 are exactly identical! WARNING: Sequences tr_A0A2D0PIP5_A0A2D0PIP5_ICTPU_7998 and tr_A0A2D0PL20_A0A2D0PL20_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0QYS8_A0A2D0QYS8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0QYT3_A0A2D0QYT3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0QZ12_A0A2D0QZ12_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0QZ17_A0A2D0QZ17_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0R0K1_A0A2D0R0K1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0R0L3_A0A2D0R0L3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0R1A8_A0A2D0R1A8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYS2_A0A2D0QYS2_ICTPU_7998 and tr_A0A2D0R1B5_A0A2D0R1B5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYT2_A0A2D0QYT2_ICTPU_7998 and tr_A0A2D0QYU4_A0A2D0QYU4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYT2_A0A2D0QYT2_ICTPU_7998 and tr_A0A2D0QZ23_A0A2D0QZ23_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYT2_A0A2D0QYT2_ICTPU_7998 and tr_A0A2D0R0K7_A0A2D0R0K7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYU5_A0A2D0QYU5_ICTPU_7998 and tr_A0A2D0QZ28_A0A2D0QZ28_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QYU5_A0A2D0QYU5_ICTPU_7998 and tr_A0A2D0R1C3_A0A2D0R1C3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5LC48_A0A2K5LC48_CERAT_9531 and tr_A0A2K5Z3N5_A0A2K5Z3N5_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 35 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/Q6AWC2/4_raxmlng_ancestral/Q6AWC2.raxml.reduced.phy Alignment comprises 1 partitions and 1192 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1192 Gaps: 44.34 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6AWC2/4_raxmlng_ancestral/Q6AWC2.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/Q6AWC2/3_mltree/Q6AWC2.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 298 / 23840 [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: -274462.983955 [00:00:00 -274462.983955] Initial branch length optimization [00:00:02 -266273.402851] Model parameter optimization (eps = 0.100000) [00:01:30] Tree #1, final logLikelihood: -264804.433054 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.176381,0.591888) (0.093372,1.445713) (0.422629,0.622308) (0.307619,1.617613) 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/Q6AWC2/4_raxmlng_ancestral/Q6AWC2.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6AWC2/4_raxmlng_ancestral/Q6AWC2.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6AWC2/4_raxmlng_ancestral/Q6AWC2.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q6AWC2/4_raxmlng_ancestral/Q6AWC2.raxml.log Analysis started: 12-Jul-2021 18:22:04 / finished: 12-Jul-2021 18:23:45 Elapsed time: 100.991 seconds Consumed energy: 8.338 Wh