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 02-Jun-2021 14:47:59 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q12840/2_msa/Q12840_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q12840/3_mltree/Q12840.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q12840/4_raxmlng_ancestral/Q12840 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622634479 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/Q12840/2_msa/Q12840_nogap_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1032 sites WARNING: Sequences tr_B4QHV8_B4QHV8_DROSI_7240 and tr_B4HSU7_B4HSU7_DROSE_7238 are exactly identical! WARNING: Sequences tr_M3XWT1_M3XWT1_MUSPF_9669 and tr_A0A2Y9IXM0_A0A2Y9IXM0_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YNP9_M3YNP9_MUSPF_9669 and tr_M3WU61_M3WU61_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YNP9_M3YNP9_MUSPF_9669 and tr_A0A2Y9KJ36_A0A2Y9KJ36_ENHLU_391180 are exactly identical! WARNING: Sequences tr_J3KM97_J3KM97_COCIM_246410 and tr_E9DFX9_E9DFX9_COCPS_443226 are exactly identical! WARNING: Sequences tr_B6Q7D9_B6Q7D9_TALMQ_441960 and tr_A0A093W160_A0A093W160_TALMA_1077442 are exactly identical! WARNING: Sequences tr_G3RC75_G3RC75_GORGO_9595 and tr_H2R425_H2R425_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RC75_G3RC75_GORGO_9595 and tr_A0A2R9A2Q6_A0A2R9A2Q6_PANPA_9597 are exactly identical! WARNING: Sequences sp_P48467_KINH_NEUCR_367110 and tr_G4UIC7_G4UIC7_NEUT9_510952 are exactly identical! WARNING: Sequences tr_A0A2I3SNT1_A0A2I3SNT1_PANTR_9598 and sp_O60282_KIF5C_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3SNT1_A0A2I3SNT1_PANTR_9598 and tr_A0A2R9AM90_A0A2R9AM90_PANPA_9597 are exactly identical! WARNING: Sequences tr_F9FNR5_F9FNR5_FUSOF_660025 and tr_X0C4Q5_X0C4Q5_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FNR5_F9FNR5_FUSOF_660025 and tr_A0A2H3TNF1_A0A2H3TNF1_FUSOX_5507 are exactly identical! WARNING: Sequences tr_F9FNR5_F9FNR5_FUSOF_660025 and tr_A0A2H3HP41_A0A2H3HP41_FUSOX_327505 are exactly identical! WARNING: Sequences sp_Q12840_KIF5A_HUMAN_9606 and tr_A0A1D5RBX9_A0A1D5RBX9_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q12840_KIF5A_HUMAN_9606 and tr_G7PIV7_G7PIV7_MACFA_9541 are exactly identical! WARNING: Sequences sp_Q12840_KIF5A_HUMAN_9606 and tr_A0A2I3ML31_A0A2I3ML31_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q12840_KIF5A_HUMAN_9606 and tr_A0A2K5YNQ6_A0A2K5YNQ6_MANLE_9568 are exactly identical! WARNING: Sequences tr_A2QLG7_A2QLG7_ASPNC_425011 and tr_A0A319ALY3_A0A319ALY3_9EURO_1450533 are exactly identical! WARNING: Sequences tr_F6UPB7_F6UPB7_MACMU_9544 and tr_A0A0D9RGR4_A0A0D9RGR4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F9X021_F9X021_ZYMTI_336722 and tr_A0A1X7RDZ9_A0A1X7RDZ9_ZYMTR_1276538 are exactly identical! WARNING: Sequences tr_G2YZ80_G2YZ80_BOTF4_999810 and tr_M7UL19_M7UL19_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_F2PYE8_F2PYE8_TRIEC_559882 and tr_A0A059J2K7_A0A059J2K7_9EURO_1215338 are exactly identical! WARNING: Sequences tr_W2QAX5_W2QAX5_PHYPN_761204 and tr_A0A0W8CN37_A0A0W8CN37_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A151PCM3_A0A151PCM3_ALLMI_8496 and tr_A0A1U7S0Y8_A0A1U7S0Y8_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091VR74_A0A091VR74_NIPNI_128390 and tr_A0A087QU59_A0A087QU59_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091VR74_A0A091VR74_NIPNI_128390 and tr_A0A0A0A263_A0A0A0A263_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V0S310_A0A0V0S310_9BILA_6336 and tr_A0A0V0VFZ5_A0A0V0VFZ5_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1DBW4_A0A0V1DBW4_TRIBR_45882 and tr_A0A0V1LE92_A0A0V1LE92_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0E0SNZ9_A0A0E0SNZ9_GIBZE_229533 and tr_A0A2T4GLQ9_A0A2T4GLQ9_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A194VV77_A0A194VV77_9PEZI_105487 and tr_A0A194USZ8_A0A194USZ8_9PEZI_694573 are exactly identical! WARNING: Sequences tr_A0A2D0S765_A0A2D0S765_ICTPU_7998 and tr_W5UD21_W5UD21_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A319C296_A0A319C296_9EURO_1448315 and tr_A0A2V5H907_A0A2V5H907_9EURO_1450538 are exactly identical! WARNING: Duplicate sequences found: 33 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/Q12840/4_raxmlng_ancestral/Q12840.raxml.reduced.phy Alignment comprises 1 partitions and 1032 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 1032 Gaps: 20.25 % Invariant sites: 0.68 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q12840/4_raxmlng_ancestral/Q12840.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/Q12840/3_mltree/Q12840.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 258 / 20640 [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: -317186.914660 [00:00:00 -317186.914660] Initial branch length optimization [00:00:02 -316547.961433] Model parameter optimization (eps = 0.100000) [00:00:53] Tree #1, final logLikelihood: -316080.210656 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.157787,0.188988) (0.146886,0.323020) (0.388757,0.760475) (0.306570,2.045514) 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/Q12840/4_raxmlng_ancestral/Q12840.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q12840/4_raxmlng_ancestral/Q12840.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q12840/4_raxmlng_ancestral/Q12840.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q12840/4_raxmlng_ancestral/Q12840.raxml.log Analysis started: 02-Jun-2021 14:47:59 / finished: 02-Jun-2021 14:49:02 Elapsed time: 63.161 seconds