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 18:37:00 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49810/2_msa/P49810_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49810/3_mltree/P49810.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49810/4_raxmlng_ancestral/P49810 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622648220 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/P49810/2_msa/P49810_nogap_msa.fasta [00:00:00] Loaded alignment with 620 taxa and 448 sites WARNING: Sequences tr_B4QRZ4_B4QRZ4_DROSI_7240 and tr_B4IAA8_B4IAA8_DROSE_7238 are exactly identical! WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_H2Q8K1_H2Q8K1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and sp_P49768_PSN1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_F7AGU8_F7AGU8_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_G7PAT1_G7PAT1_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_A0A0D9RK10_A0A0D9RK10_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_A0A2K5N1F1_A0A2K5N1F1_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_A0A2K6CVX6_A0A2K6CVX6_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_A0A2K5YUS1_A0A2K5YUS1_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1QRH5_G1QRH5_NOMLE_61853 and tr_A0A2R9BSY5_A0A2R9BSY5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QLC6_G3QLC6_GORGO_9595 and sp_P49810_PSN2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8U215_A0A2J8U215_PONAB_9601 and tr_A0A0D9RUZ9_A0A0D9RUZ9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A0R3P728_A0A0R3P728_DROPS_46245 and tr_B4H7M0_B4H7M0_DROPE_7234 are exactly identical! WARNING: Sequences tr_H2R821_H2R821_PANTR_9598 and tr_A0A2R9A5I7_A0A2R9A5I7_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A158NMP7_A0A158NMP7_ATTCE_12957 and tr_A0A151JTA9_A0A151JTA9_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A0E0FK13_A0A0E0FK13_ORYNI_4536 and tr_A0A0E0MUL4_A0A0E0MUL4_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0GQC9_A0A0E0GQC9_ORYNI_4536 and tr_C7J054_C7J054_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_F7A2E1_F7A2E1_MACMU_9544 and tr_A0A096MR14_A0A096MR14_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7A2E1_F7A2E1_MACMU_9544 and tr_A0A2K6CMA8_A0A2K6CMA8_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7A2E1_F7A2E1_MACMU_9544 and tr_A0A2K5XVZ1_A0A2K5XVZ1_MANLE_9568 are exactly identical! WARNING: Sequences tr_M4DPB3_M4DPB3_BRARP_51351 and tr_A0A078J4P4_A0A078J4P4_BRANA_3708 are exactly identical! WARNING: Sequences tr_W2PU42_W2PU42_PHYPN_761204 and tr_W2GC38_W2GC38_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2QBN6_W2QBN6_PHYPN_761204 and tr_W2LA02_W2LA02_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A015ICJ2_A0A015ICJ2_9GLOM_1432141 and tr_U9UMQ1_U9UMQ1_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A067FHZ3_A0A067FHZ3_CITSI_2711 and tr_A0A2H5QAG8_A0A2H5QAG8_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0D2LVY9_A0A0D2LVY9_GOSRA_29730 and tr_A0A1U8P253_A0A1U8P253_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0K0FPP6_A0A0K0FPP6_STRVS_75913 and tr_A0A0N5B409_A0A0N5B409_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A0V0X6A8_A0A0V0X6A8_9BILA_92179 and tr_A0A0V0UQH5_A0A0V0UQH5_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V0X6A8_A0A0V0X6A8_9BILA_92179 and tr_A0A0V1LU29_A0A0V1LU29_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0X6A8_A0A0V0X6A8_9BILA_92179 and tr_A0A0V1NV59_A0A0V1NV59_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0X6A8_A0A0V0X6A8_9BILA_92179 and tr_A0A0V0TJL5_A0A0V0TJL5_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S3XK05_A0A1S3XK05_TOBAC_4097 and tr_A0A1U7VCP0_A0A1U7VCP0_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3ZTL3_A0A1S3ZTL3_TOBAC_4097 and tr_A0A1U7VRH0_A0A1U7VRH0_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1Y1XJK0_A0A1Y1XJK0_9FUNG_1314790 and tr_A0A1Y1Y376_A0A1Y1Y376_9FUNG_1314790 are exactly identical! WARNING: Sequences tr_A0A2U4A8E9_A0A2U4A8E9_TURTR_9739 and tr_A0A2Y9NSH6_A0A2Y9NSH6_DELLE_9749 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/020621_run/phylogeny-snakemake/results/P49810/4_raxmlng_ancestral/P49810.raxml.reduced.phy Alignment comprises 1 partitions and 448 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 448 Gaps: 21.53 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49810/4_raxmlng_ancestral/P49810.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/P49810/3_mltree/P49810.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 112 / 8960 [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: -125414.294306 [00:00:00 -125414.294306] Initial branch length optimization [00:00:01 -124931.997877] Model parameter optimization (eps = 0.100000) [00:00:38] Tree #1, final logLikelihood: -124164.859211 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.255298,0.350209) (0.190087,0.586400) (0.286743,0.705375) (0.267872,2.228170) 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/P49810/4_raxmlng_ancestral/P49810.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49810/4_raxmlng_ancestral/P49810.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49810/4_raxmlng_ancestral/P49810.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P49810/4_raxmlng_ancestral/P49810.raxml.log Analysis started: 02-Jun-2021 18:37:00 / finished: 02-Jun-2021 18:37:41 Elapsed time: 41.266 seconds Consumed energy: 3.735 Wh