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 14:10:55 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O95259/2_msa/O95259_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O95259/3_mltree/O95259.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O95259/4_raxmlng_ancestral/O95259 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622805055 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/O95259/2_msa/O95259_nogap_msa.fasta [00:00:00] Loaded alignment with 1000 taxa and 989 sites WARNING: Sequences tr_A1ZB14_A1ZB14_DROME_7227 and tr_B4HN99_B4HN99_DROSE_7238 are exactly identical! WARNING: Sequences tr_G3RMV3_G3RMV3_GORGO_9595 and tr_H2PBC8_H2PBC8_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3RMV3_G3RMV3_GORGO_9595 and tr_A0A2I3S5Z0_A0A2I3S5Z0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SKG7_G3SKG7_GORGO_9595 and tr_H2Q129_H2Q129_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3SKG7_G3SKG7_GORGO_9595 and sp_O95259_KCNH1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3SKG7_G3SKG7_GORGO_9595 and tr_A0A2R9CDK7_A0A2R9CDK7_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3SKT9_G3SKT9_GORGO_9595 and sp_Q8NCM2_KCNH5_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2NH75_H2NH75_PONAB_9601 and tr_H2Q5V5_H2Q5V5_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2NH75_H2NH75_PONAB_9601 and sp_Q9ULD8_KCNH3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2NH75_H2NH75_PONAB_9601 and tr_A0A2R9ANM2_A0A2R9ANM2_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QIW5_H2QIW5_PANTR_9598 and tr_A0A2R9AYY0_A0A2R9AYY0_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R4V4_H2R4V4_PANTR_9598 and sp_Q12809_KCNH2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2R9B0_H2R9B0_PANTR_9598 and tr_A0A2R8ZTW0_A0A2R8ZTW0_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6WEE3_F6WEE3_MACMU_9544 and tr_A0A096NPA8_A0A096NPA8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6WEE3_F6WEE3_MACMU_9544 and tr_A0A2K5MTB3_A0A2K5MTB3_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7DXE4_F7DXE4_MACMU_9544 and tr_G7PAH7_G7PAH7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7DXE4_F7DXE4_MACMU_9544 and tr_A0A096NVJ8_A0A096NVJ8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7DXE4_F7DXE4_MACMU_9544 and tr_A0A2K6DGC9_A0A2K6DGC9_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7DXE4_F7DXE4_MACMU_9544 and tr_A0A2K6A9C2_A0A2K6A9C2_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7GL26_F7GL26_MACMU_9544 and tr_A0A0D9RS01_A0A0D9RS01_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7GL26_F7GL26_MACMU_9544 and tr_A0A2K5NA49_A0A2K5NA49_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7GL26_F7GL26_MACMU_9544 and tr_A0A2K6BR64_A0A2K6BR64_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GUN6_F7GUN6_MACMU_9544 and tr_G7NY23_G7NY23_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GUN6_F7GUN6_MACMU_9544 and tr_A0A2K5LPE3_A0A2K5LPE3_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3SVQ7_G3SVQ7_LOXAF_9785 and tr_A0A2Y9DAD7_A0A2Y9DAD7_TRIMA_127582 are exactly identical! WARNING: Sequences tr_B3RQL4_B3RQL4_TRIAD_10228 and tr_A0A369S7P7_A0A369S7P7_9METZ_287889 are exactly identical! WARNING: Sequences tr_A0A044UED0_A0A044UED0_ONCVO_6282 and tr_A0A182E9X1_A0A182E9X1_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A096MP06_A0A096MP06_PAPAN_9555 and tr_A0A2K5LNA9_A0A2K5LNA9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096MP06_A0A096MP06_PAPAN_9555 and tr_A0A2K6B3Q4_A0A2K6B3Q4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096N8P3_A0A096N8P3_PAPAN_9555 and tr_A0A2K5Z1C5_A0A2K5Z1C5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A096P5S0_A0A096P5S0_PAPAN_9555 and tr_A0A2K6CKY2_A0A2K6CKY2_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3MBJ1_A0A2I3MBJ1_PAPAN_9555 and tr_A0A2K6AGR2_A0A2K6AGR2_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0V1L9D4_A0A0V1L9D4_9BILA_6335 and tr_A0A0V1NMC9_A0A0V1NMC9_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A195BDL1_A0A195BDL1_9HYME_520822 and tr_A0A151JYL6_A0A151JYL6_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A2D0RQ54_A0A2D0RQ54_ICTPU_7998 and tr_A0A2D0RQ68_A0A2D0RQ68_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T289_A0A2D0T289_ICTPU_7998 and tr_A0A2D0T3F4_A0A2D0T3F4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T5E0_A0A2D0T5E0_ICTPU_7998 and tr_W5UCW3_W5UCW3_ICTPU_7998 are exactly identical! WARNING: Duplicate sequences found: 37 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/O95259/4_raxmlng_ancestral/O95259.raxml.reduced.phy Alignment comprises 1 partitions and 989 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 989 Gaps: 25.75 % Invariant sites: 0.20 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O95259/4_raxmlng_ancestral/O95259.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/O95259/3_mltree/O95259.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 248 / 19840 [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: -276897.791881 [00:00:00 -276897.791881] Initial branch length optimization [00:00:02 -229534.475531] Model parameter optimization (eps = 0.100000) [00:01:05] Tree #1, final logLikelihood: -228517.325476 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.220985,0.225828) (0.194313,0.268365) (0.275250,0.712197) (0.309451,2.268262) 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/O95259/4_raxmlng_ancestral/O95259.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O95259/4_raxmlng_ancestral/O95259.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O95259/4_raxmlng_ancestral/O95259.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O95259/4_raxmlng_ancestral/O95259.raxml.log Analysis started: 04-Jun-2021 14:10:55 / finished: 04-Jun-2021 14:12:09 Elapsed time: 74.174 seconds