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 22:49:34 as follows: raxml-ng --ancestral --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y619/2_msa/Q9Y619_nogap_msa.fasta --tree /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y619/3_mltree/Q9Y619.raxml.bestTree_unrooted --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y619/4_raxmlng_ancestral/Q9Y619 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622663374 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/Q9Y619/2_msa/Q9Y619_nogap_msa.fasta [00:00:00] Loaded alignment with 1000 taxa and 301 sites WARNING: Sequences tr_A0A2I3H4B1_A0A2I3H4B1_NOMLE_61853 and tr_H2QMK3_H2QMK3_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3H4B1_A0A2I3H4B1_NOMLE_61853 and sp_O43772_MCAT_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3H4B1_A0A2I3H4B1_NOMLE_61853 and tr_A0A2R9AMS5_A0A2R9AMS5_PANPA_9597 are exactly identical! WARNING: Sequences tr_Q29P34_Q29P34_DROPS_46245 and tr_B4GJZ5_B4GJZ5_DROPE_7234 are exactly identical! WARNING: Sequences tr_H2Q7G6_H2Q7G6_PANTR_9598 and tr_A0A2R9AKQ6_A0A2R9AKQ6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A158NRS0_A0A158NRS0_ATTCE_12957 and tr_A0A195BR34_A0A195BR34_9HYME_520822 are exactly identical! WARNING: Sequences sp_Q9Y619_ORNT1_HUMAN_9606 and tr_A0A0D9RZ22_A0A0D9RZ22_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q9Y619_ORNT1_HUMAN_9606 and tr_A0A2K5P6W1_A0A2K5P6W1_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6Q4M5_F6Q4M5_MACMU_9544 and tr_G7NXV5_G7NXV5_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6Q4M5_F6Q4M5_MACMU_9544 and tr_A0A096NF18_A0A096NF18_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6Q4M5_F6Q4M5_MACMU_9544 and tr_A0A2K5M165_A0A2K5M165_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6Q4M5_F6Q4M5_MACMU_9544 and tr_A0A2K5ZWK9_A0A2K5ZWK9_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6T3V1_F6T3V1_MACMU_9544 and tr_A0A096NC50_A0A096NC50_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A2ZAH7_A2ZAH7_ORYSI_39946 and tr_I1QW70_I1QW70_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A2ZAH7_A2ZAH7_ORYSI_39946 and tr_A3C7K0_A3C7K0_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1QW69_I1QW69_ORYGL_4538 and tr_Q7XBY4_Q7XBY4_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_G7PW31_G7PW31_MACFA_9541 and tr_A0A2K6DUW3_A0A2K6DUW3_MACNE_9545 are exactly identical! WARNING: Sequences tr_M4DLZ3_M4DLZ3_BRARP_51351 and tr_A0A078HBR1_A0A078HBR1_BRANA_3708 are exactly identical! WARNING: Sequences tr_S2K7W5_S2K7W5_MUCC1_1220926 and tr_A0A168Q2Z5_A0A168Q2Z5_MUCCL_747725 are exactly identical! WARNING: Sequences tr_V2XDG6_V2XDG6_MONRO_1381753 and tr_A0A0W0EYL5_A0A0W0EYL5_9AGAR_221103 are exactly identical! WARNING: Sequences tr_W2PN53_W2PN53_PHYPN_761204 and tr_A0A0W8D1B6_A0A0W8D1B6_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2PN53_W2PN53_PHYPN_761204 and tr_W2MMM8_W2MMM8_PHYPR_4792 are exactly identical! WARNING: Sequences tr_W2QAM7_W2QAM7_PHYPN_761204 and tr_A0A0W8DVW6_A0A0W8DVW6_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2QAM7_W2QAM7_PHYPN_761204 and tr_W2GY83_W2GY83_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A3B5XZD5_A0A3B5XZD5_WHEAT_4565 and tr_A0A3B5ZU90_A0A3B5ZU90_WHEAT_4565 are exactly identical! WARNING: Sequences tr_V4UQ90_V4UQ90_9ROSI_85681 and tr_A0A2H5QMB4_A0A2H5QMB4_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0A1NV72_A0A0A1NV72_9FUNG_58291 and tr_A0A367JH20_A0A367JH20_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0A1NZJ3_A0A0A1NZJ3_9FUNG_58291 and tr_A0A2G4T5D7_A0A2G4T5D7_9FUNG_1340429 are exactly identical! WARNING: Sequences tr_A0A0A1NZJ3_A0A0A1NZJ3_9FUNG_58291 and tr_A0A367K9C2_A0A367K9C2_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0W8C9M2_A0A0W8C9M2_PHYNI_4790 and tr_W2L486_W2L486_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A091JHB7_A0A091JHB7_EGRGA_188379 and tr_A0A087QM46_A0A087QM46_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A0L0RXJ3_A0A0L0RXJ3_ALLMA_578462 and tr_A0A0L0S2A6_A0A0L0S2A6_ALLMA_578462 are exactly identical! WARNING: Sequences tr_A0A0V0WK15_A0A0V0WK15_9BILA_92179 and tr_A0A0V1PD72_A0A0V1PD72_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V0WK15_A0A0V0WK15_9BILA_92179 and tr_A0A0V0TNY3_A0A0V0TNY3_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A165EJD4_A0A165EJD4_EXIGL_1314781 and tr_A0A165K195_A0A165K195_EXIGL_1314781 are exactly identical! WARNING: Sequences tr_A0A1S4DAN8_A0A1S4DAN8_TOBAC_4097 and tr_A0A1U7VAA3_A0A1U7VAA3_NICSY_4096 are exactly identical! WARNING: Sequences tr_B5X1L1_B5X1L1_SALSA_8030 and tr_A0A060W756_A0A060W756_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A2U4BGC9_A0A2U4BGC9_TURTR_9739 and tr_A0A2Y9NMA2_A0A2Y9NMA2_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 38 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/Q9Y619/4_raxmlng_ancestral/Q9Y619.raxml.reduced.phy Alignment comprises 1 partitions and 301 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 301 Gaps: 8.55 % Invariant sites: 0.66 % NOTE: Binary MSA file already exists: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y619/4_raxmlng_ancestral/Q9Y619.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/Q9Y619/3_mltree/Q9Y619.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 76 / 6080 [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: -179284.485185 [00:00:00 -179284.485185] Initial branch length optimization [00:00:01 -170370.911813] Model parameter optimization (eps = 0.100000) [00:00:36] Tree #1, final logLikelihood: -169645.030506 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.201091,0.364030) (0.340313,0.508401) (0.311115,1.361447) (0.147480,2.239041) 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/Q9Y619/4_raxmlng_ancestral/Q9Y619.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y619/4_raxmlng_ancestral/Q9Y619.raxml.ancestralStates Node-labeled tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y619/4_raxmlng_ancestral/Q9Y619.raxml.ancestralTree Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_020621/phylogeny-snakemake/results/Q9Y619/4_raxmlng_ancestral/Q9Y619.raxml.log Analysis started: 02-Jun-2021 22:49:34 / finished: 02-Jun-2021 22:50:13 Elapsed time: 38.934 seconds