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 13:57:10 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43586/2_msa/O43586_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43586/3_mltree/O43586.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43586/4_raxmlng_ancestral/O43586 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622804230 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/O43586/2_msa/O43586_nogap_msa.fasta [00:00:00] Loaded alignment with 979 taxa and 416 sites WARNING: Sequences tr_B4QMK8_B4QMK8_DROSI_7240 and sp_P13395_SPTCA_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QMK8_B4QMK8_DROSI_7240 and tr_B4HW03_B4HW03_DROSE_7238 are exactly identical! WARNING: Sequences tr_G1RLN4_G1RLN4_NOMLE_61853 and tr_G3QXE8_G3QXE8_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RLN4_G1RLN4_NOMLE_61853 and tr_H2Q9I8_H2Q9I8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RLN4_G1RLN4_NOMLE_61853 and sp_Q12965_MYO1E_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3S2M2_G3S2M2_GORGO_9595 and sp_O00160_MYO1F_HUMAN_9606 are exactly identical! WARNING: Sequences tr_B8N1V4_B8N1V4_ASPFN_332952 and tr_A0A1S9DMS3_A0A1S9DMS3_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A179UTI6_A0A179UTI6_BLAGS_559298 and tr_C5G9M9_C5G9M9_AJEDR_559297 are exactly identical! WARNING: Sequences tr_H2QUR6_H2QUR6_PANTR_9598 and sp_P14598_NCF1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QUR6_H2QUR6_PANTR_9598 and tr_A0A2R9AJ30_A0A2R9AJ30_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R6E1_H2R6E1_PANTR_9598 and tr_A0A2R9AJV3_A0A2R9AJV3_PANPA_9597 are exactly identical! WARNING: Sequences tr_I3LYB6_I3LYB6_ICTTR_43179 and tr_A0A337SPL1_A0A337SPL1_FELCA_9685 are exactly identical! WARNING: Sequences tr_A0A1D5QE98_A0A1D5QE98_MACMU_9544 and tr_A0A2I3LHH9_A0A2I3LHH9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5QE98_A0A1D5QE98_MACMU_9544 and tr_A0A2K5MY70_A0A2K5MY70_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5QE98_A0A1D5QE98_MACMU_9544 and tr_A0A2K6CM60_A0A2K6CM60_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5RAL5_A0A1D5RAL5_MACMU_9544 and tr_E1BFB0_E1BFB0_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A1D5RAL5_A0A1D5RAL5_MACMU_9544 and tr_A0A2I3MUN3_A0A2I3MUN3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5RAL5_A0A1D5RAL5_MACMU_9544 and tr_A0A0D9RP68_A0A0D9RP68_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5RAL5_A0A1D5RAL5_MACMU_9544 and tr_A0A2K5MZP7_A0A2K5MZP7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5RAL5_A0A1D5RAL5_MACMU_9544 and tr_A0A2K6C6N1_A0A2K6C6N1_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6RKD2_F6RKD2_MACMU_9544 and tr_G7PBK7_G7PBK7_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6RKD2_F6RKD2_MACMU_9544 and tr_A0A096NM83_A0A096NM83_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6RKD2_F6RKD2_MACMU_9544 and tr_A0A2K6ANI5_A0A2K6ANI5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6RKD2_F6RKD2_MACMU_9544 and tr_A0A2K5XXV5_A0A2K5XXV5_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6SL33_F6SL33_MACMU_9544 and tr_G7P186_G7P186_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6SL33_F6SL33_MACMU_9544 and tr_A0A096MQ72_A0A096MQ72_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6SL33_F6SL33_MACMU_9544 and tr_A0A2K6C2W4_A0A2K6C2W4_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6SL33_F6SL33_MACMU_9544 and tr_A0A2K5Z934_A0A2K5Z934_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7MYE5_G7MYE5_MACMU_9544 and tr_A0A2K5KJL5_A0A2K5KJL5_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7MYE5_G7MYE5_MACMU_9544 and tr_A0A2K6BGZ2_A0A2K6BGZ2_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7MYE5_G7MYE5_MACMU_9544 and tr_A0A2K5ZEW2_A0A2K5ZEW2_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A1B8XYK0_A0A1B8XYK0_XENTR_8364 and tr_F6Z0C4_F6Z0C4_XENTR_8364 are exactly identical! WARNING: Sequences tr_G2YKU3_G2YKU3_BOTF4_999810 and tr_M7U5U1_M7U5U1_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_D2HV90_D2HV90_AILME_9646 and tr_A0A3Q0E2U6_A0A3Q0E2U6_TARSY_1868482 are exactly identical! WARNING: Sequences tr_A0A0M9WGT6_A0A0M9WGT6_9EURO_229535 and tr_A0A0G4P9N3_A0A0G4P9N3_PENCA_1429867 are exactly identical! WARNING: Sequences tr_A0A091JS43_A0A091JS43_EGRGA_188379 and tr_A0A091VNV6_A0A091VNV6_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JS43_A0A091JS43_EGRGA_188379 and tr_A0A087REM2_A0A087REM2_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A2D0QTR2_A0A2D0QTR2_ICTPU_7998 and tr_A0A2D0QWE5_A0A2D0QWE5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SRP5_A0A2D0SRP5_ICTPU_7998 and tr_A0A2D0SRP7_A0A2D0SRP7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2S7QH73_A0A2S7QH73_9HELO_2070414 and tr_A0A2S7PKN0_A0A2S7PKN0_9HELO_2070412 are exactly identical! WARNING: Sequences tr_A0A2U4A8Y3_A0A2U4A8Y3_TURTR_9739 and tr_Q9N0E8_Q9N0E8_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4CH51_A0A2U4CH51_TURTR_9739 and tr_A0A2Y9NXB5_A0A2Y9NXB5_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 42 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/O43586/4_raxmlng_ancestral/O43586.raxml.reduced.phy Alignment comprises 1 partitions and 416 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 416 Gaps: 36.64 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43586/4_raxmlng_ancestral/O43586.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/O43586/3_mltree/O43586.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 104 / 8320 [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: -237193.093828 [00:00:00 -237193.093828] Initial branch length optimization [00:00:01 -185989.444454] Model parameter optimization (eps = 0.100000) [00:00:56] Tree #1, final logLikelihood: -185106.786058 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.107381,0.896248) (0.096959,0.810870) (0.364783,0.715804) (0.430877,1.309018) 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/O43586/4_raxmlng_ancestral/O43586.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43586/4_raxmlng_ancestral/O43586.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43586/4_raxmlng_ancestral/O43586.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/O43586/4_raxmlng_ancestral/O43586.raxml.log Analysis started: 04-Jun-2021 13:57:10 / finished: 04-Jun-2021 13:58:10 Elapsed time: 59.812 seconds