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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 04-Jun-2021 13:41:14 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9P202/2_msa/Q9P202_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9P202/3_mltree/Q9P202.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9P202/4_raxmlng_ancestral/Q9P202 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622803274 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9P202/2_msa/Q9P202_nogap_msa.fasta [00:00:00] Loaded alignment with 947 taxa and 907 sites WARNING: Sequences tr_B4QJH3_B4QJH3_DROSI_7240 and tr_B4HH88_B4HH88_DROSE_7238 are exactly identical! WARNING: Sequences sp_P70175_DLG3_MOUSE_10090 and sp_Q62936_DLG3_RAT_10116 are exactly identical! WARNING: Sequences sp_Q62108_DLG4_MOUSE_10090 and sp_P78352_DLG4_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q62108_DLG4_MOUSE_10090 and tr_G5B5A1_G5B5A1_HETGA_10181 are exactly identical! WARNING: Sequences sp_Q62108_DLG4_MOUSE_10090 and tr_F1MM66_F1MM66_BOVIN_9913 are exactly identical! WARNING: Sequences sp_Q62108_DLG4_MOUSE_10090 and tr_A0A0D9RHZ8_A0A0D9RHZ8_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q62108_DLG4_MOUSE_10090 and tr_A0A2Y9EEN8_A0A2Y9EEN8_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G1MRU8_G1MRU8_MELGA_9103 and tr_A0A0Q3M215_A0A0Q3M215_AMAAE_12930 are exactly identical! WARNING: Sequences tr_A0A2I3SQG1_A0A2I3SQG1_PANTR_9598 and tr_A0A1D5Q4X6_A0A1D5Q4X6_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3SQG1_A0A2I3SQG1_PANTR_9598 and tr_A0A2I3M620_A0A2I3M620_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3SQG1_A0A2I3SQG1_PANTR_9598 and tr_A0A0D9S1V3_A0A0D9S1V3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3SQG1_A0A2I3SQG1_PANTR_9598 and tr_A0A2K6APC6_A0A2K6APC6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3SQG1_A0A2I3SQG1_PANTR_9598 and tr_A0A2K5YJ32_A0A2K5YJ32_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2QC23_H2QC23_PANTR_9598 and tr_F6Z588_F6Z588_CALJA_9483 are exactly identical! WARNING: Sequences tr_H2QC23_H2QC23_PANTR_9598 and tr_A0A096P2M8_A0A096P2M8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2QC23_H2QC23_PANTR_9598 and tr_A0A1S2ZMU4_A0A1S2ZMU4_ERIEU_9365 are exactly identical! WARNING: Sequences tr_H2QC23_H2QC23_PANTR_9598 and tr_A0A3Q0E6A6_A0A3Q0E6A6_TARSY_1868482 are exactly identical! WARNING: Sequences tr_H2QC23_H2QC23_PANTR_9598 and tr_A0A2K5KLX8_A0A2K5KLX8_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2QC23_H2QC23_PANTR_9598 and tr_A0A2K6AMA3_A0A2K6AMA3_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2QC23_H2QC23_PANTR_9598 and tr_A0A2K5ZWB0_A0A2K5ZWB0_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2QC23_H2QC23_PANTR_9598 and tr_A0A2R9BJ13_A0A2R9BJ13_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A3B5Q5A3_A0A3B5Q5A3_XIPMA_8083 and tr_A0A087YNA4_A0A087YNA4_POEFO_48698 are exactly identical! WARNING: Sequences sp_Q9Y4G8_RPGF2_HUMAN_9606 and tr_G8F2H7_G8F2H7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6UBK1_F6UBK1_MACMU_9544 and tr_A0A096NFW2_A0A096NFW2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HST7_F7HST7_MACMU_9544 and tr_G7P874_G7P874_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3N2P1_A0A2I3N2P1_PAPAN_9555 and tr_A0A2K6ATZ3_A0A2K6ATZ3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A091EQF5_A0A091EQF5_CORBR_85066 and tr_A0A091IN14_A0A091IN14_EGRGA_188379 are exactly identical! WARNING: Sequences tr_A0A091EQF5_A0A091EQF5_CORBR_85066 and tr_A0A091WN12_A0A091WN12_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091EQF5_A0A091EQF5_CORBR_85066 and tr_A0A091GBK3_A0A091GBK3_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091WGB6_A0A091WGB6_NIPNI_128390 and tr_A0A091HZ62_A0A091HZ62_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A2D0RY89_A0A2D0RY89_ICTPU_7998 and tr_A0A2D0RY98_A0A2D0RY98_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RY89_A0A2D0RY89_ICTPU_7998 and tr_A0A2D0RZ58_A0A2D0RZ58_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RYA5_A0A2D0RYA5_ICTPU_7998 and tr_A0A2D0RZU2_A0A2D0RZU2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RZ63_A0A2D0RZ63_ICTPU_7998 and tr_A0A2D0RZT7_A0A2D0RZT7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5LJB3_A0A2K5LJB3_CERAT_9531 and tr_A0A2K6BMH2_A0A2K6BMH2_MACNE_9545 are exactly identical! WARNING: Duplicate sequences found: 35 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9P202/4_raxmlng_ancestral/Q9P202.raxml.reduced.phy Alignment comprises 1 partitions and 907 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 907 Gaps: 45.63 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9P202/4_raxmlng_ancestral/Q9P202.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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9P202/3_mltree/Q9P202.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 227 / 18160 [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: -369859.315110 [00:00:00 -369859.315110] Initial branch length optimization [00:00:02 -279499.273623] Model parameter optimization (eps = 0.100000) [00:01:21] Tree #1, final logLikelihood: -278703.473305 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.060280,0.358705) (0.065095,0.360148) (0.409087,0.725205) (0.465538,1.413981) 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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9P202/4_raxmlng_ancestral/Q9P202.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9P202/4_raxmlng_ancestral/Q9P202.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9P202/4_raxmlng_ancestral/Q9P202.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9P202/4_raxmlng_ancestral/Q9P202.raxml.log Analysis started: 04-Jun-2021 13:41:14 / finished: 04-Jun-2021 13:42:43 Elapsed time: 89.078 seconds