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 02:44:37 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04181/2_msa/P04181_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04181/3_mltree/P04181.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04181/4_raxmlng_ancestral/P04181 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622677477 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/P04181/2_msa/P04181_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 439 sites WARNING: Sequences tr_J3K4I1_J3K4I1_COCIM_246410 and tr_A0A0J7B8P5_A0A0J7B8P5_COCIT_404692 are exactly identical! WARNING: Sequences tr_B6QL62_B6QL62_TALMQ_441960 and tr_A0A093VIW0_A0A093VIW0_TALMA_1077442 are exactly identical! WARNING: Sequences tr_B2W006_B2W006_PYRTR_426418 and tr_A0A2W1GVL0_A0A2W1GVL0_9PLEO_45151 are exactly identical! WARNING: Sequences tr_A0A179UUX5_A0A179UUX5_BLAGS_559298 and tr_C5GWJ3_C5GWJ3_AJEDR_559297 are exactly identical! WARNING: Sequences tr_H2Q2Q6_H2Q2Q6_PANTR_9598 and sp_P04181_OAT_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2Q2Q6_H2Q2Q6_PANTR_9598 and tr_A0A2R9B3M7_A0A2R9B3M7_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9G952_F9G952_FUSOF_660025 and tr_A0A0D2XZB9_A0A0D2XZB9_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9G952_F9G952_FUSOF_660025 and tr_N4USZ2_N4USZ2_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9G952_F9G952_FUSOF_660025 and tr_A0A2H3THR4_A0A2H3THR4_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9G952_F9G952_FUSOF_660025 and tr_A0A2H3GJK0_A0A2H3GJK0_FUSOX_327505 are exactly identical! WARNING: Sequences tr_E9EU01_E9EU01_METRA_655844 and tr_A0A0D9NRY4_A0A0D9NRY4_METAN_1291518 are exactly identical! WARNING: Sequences tr_J5JLJ2_J5JLJ2_BEAB2_655819 and tr_A0A0A2VJ60_A0A0A2VJ60_BEABA_1245745 are exactly identical! WARNING: Sequences tr_A0A158NUB8_A0A158NUB8_ATTCE_12957 and tr_A0A195BBN8_A0A195BBN8_9HYME_520822 are exactly identical! WARNING: Sequences tr_Q2UH16_Q2UH16_ASPOR_510516 and tr_A0A1S9DZ52_A0A1S9DZ52_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_Q2UH85_Q2UH85_ASPOR_510516 and tr_A0A1S9DYK1_A0A1S9DYK1_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A0E0G4H9_A0A0E0G4H9_ORYNI_4536 and sp_Q10G56_OAT_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A2QXG4_A2QXG4_ASPNC_425011 and tr_A0A319AR27_A0A319AR27_9EURO_1450533 are exactly identical! WARNING: Sequences tr_F7BGE6_F7BGE6_MACMU_9544 and tr_A0A2K5NZR8_A0A2K5NZR8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7BGE6_F7BGE6_MACMU_9544 and tr_A0A2K6E4K1_A0A2K6E4K1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7BGE6_F7BGE6_MACMU_9544 and tr_A0A2K5YPN7_A0A2K5YPN7_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7X7T0_G7X7T0_ASPKW_1033177 and tr_A0A100IAP9_A0A100IAP9_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7X7T0_G7X7T0_ASPKW_1033177 and tr_A0A146FKS4_A0A146FKS4_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7X7T0_G7X7T0_ASPKW_1033177 and tr_A0A1L9MWC6_A0A1L9MWC6_ASPTU_767770 are exactly identical! WARNING: Sequences tr_B8ANL7_B8ANL7_ORYSI_39946 and tr_A0A0E0NYS9_A0A0E0NYS9_ORYRU_4529 are exactly identical! WARNING: Sequences tr_F4PCC3_F4PCC3_BATDJ_684364 and tr_A0A177WYS2_A0A177WYS2_BATDE_403673 are exactly identical! WARNING: Sequences tr_F9XFW3_F9XFW3_ZYMTI_336722 and tr_A0A1X7RYL1_A0A1X7RYL1_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2XP93_G2XP93_BOTF4_999810 and tr_M7U5V6_M7U5V6_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_E3CU08_E3CU08_CAEBR_6238 and tr_A0A2G5URD4_A0A2G5URD4_9PELO_1611254 are exactly identical! WARNING: Sequences tr_F2SQI2_F2SQI2_TRIRC_559305 and tr_A0A178EWP2_A0A178EWP2_TRIRU_5551 are exactly identical! WARNING: Sequences tr_W2R7C7_W2R7C7_PHYPN_761204 and tr_A0A0W8D3W9_A0A0W8D3W9_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A094E1Q4_A0A094E1Q4_9PEZI_1420912 and tr_A0A1B8GY49_A0A1B8GY49_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0G0AF15_A0A0G0AF15_TRIHA_5544 and tr_A0A2T3ZZC2_A0A2T3ZZC2_TRIHA_983964 are exactly identical! WARNING: Sequences tr_A0A0F8UQ23_A0A0F8UQ23_9EURO_308745 and tr_A0A2T5M6K0_A0A2T5M6K0_9EURO_1392256 are exactly identical! WARNING: Sequences tr_A0A0V1D8M9_A0A0V1D8M9_TRIBR_45882 and tr_A0A0V0UV39_A0A0V0UV39_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1D8M9_A0A0V1D8M9_TRIBR_45882 and tr_A0A0V1KQ22_A0A0V1KQ22_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1D8M9_A0A0V1D8M9_TRIBR_45882 and tr_A0A0V1NGV3_A0A0V1NGV3_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1D8M9_A0A0V1D8M9_TRIBR_45882 and tr_A0A0V0TSY7_A0A0V0TSY7_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1Q3EHT5_A0A1Q3EHT5_LENED_5353 and tr_A0A1Q3EHU0_A0A1Q3EHU0_LENED_5353 are exactly identical! WARNING: Sequences tr_A0A2D0S7M8_A0A2D0S7M8_ICTPU_7998 and tr_A0A2D0S880_A0A2D0S880_ICTPU_7998 are exactly identical! WARNING: Duplicate sequences found: 39 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/P04181/4_raxmlng_ancestral/P04181.raxml.reduced.phy Alignment comprises 1 partitions and 439 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 439 Gaps: 6.65 % Invariant sites: 0.46 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04181/4_raxmlng_ancestral/P04181.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/P04181/3_mltree/P04181.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 110 / 8800 [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: -185481.782517 [00:00:00 -185481.782517] Initial branch length optimization [00:00:00 -184588.158690] Model parameter optimization (eps = 0.100000) [00:00:21] Tree #1, final logLikelihood: -183725.977544 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.288177,0.350150) (0.290840,0.433833) (0.218512,1.089585) (0.202471,2.641517) 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/P04181/4_raxmlng_ancestral/P04181.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04181/4_raxmlng_ancestral/P04181.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04181/4_raxmlng_ancestral/P04181.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P04181/4_raxmlng_ancestral/P04181.raxml.log Analysis started: 03-Jun-2021 02:44:37 / finished: 03-Jun-2021 02:45:02 Elapsed time: 25.167 seconds Consumed energy: 1.806 Wh