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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 02-Jun-2021 18:25:24 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12872/2_msa/Q12872_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12872/3_mltree/Q12872.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12872/4_raxmlng_ancestral/Q12872 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1622647524 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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12872/2_msa/Q12872_nogap_msa.fasta [00:00:00] Loaded alignment with 696 taxa and 951 sites WARNING: Sequences tr_M3YNZ0_M3YNZ0_MUSPF_9669 and tr_F1RFD3_F1RFD3_PIG_9823 are exactly identical! WARNING: Sequences tr_G1QU96_G1QU96_NOMLE_61853 and tr_G3RA68_G3RA68_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1QU96_G1QU96_NOMLE_61853 and tr_H2P414_H2P414_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1QU96_G1QU96_NOMLE_61853 and tr_H2R708_H2R708_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QU96_G1QU96_NOMLE_61853 and sp_Q15459_SF3A1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1QU96_G1QU96_NOMLE_61853 and tr_A0A096NJG8_A0A096NJG8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1QU96_G1QU96_NOMLE_61853 and tr_A0A0D9RAT5_A0A0D9RAT5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1QU96_G1QU96_NOMLE_61853 and tr_A0A2K6A644_A0A2K6A644_MANLE_9568 are exactly identical! WARNING: Sequences tr_B6QTD8_B6QTD8_TALMQ_441960 and tr_A0A093VHQ2_A0A093VHQ2_TALMA_1077442 are exactly identical! WARNING: Sequences tr_E2RDL8_E2RDL8_CANLF_9615 and tr_F6Y642_F6Y642_HORSE_9796 are exactly identical! WARNING: Sequences tr_E2RDL8_E2RDL8_CANLF_9615 and tr_H0VRD6_H0VRD6_CAVPO_10141 are exactly identical! WARNING: Sequences tr_E2RDL8_E2RDL8_CANLF_9615 and sp_A2VDN6_SF3A1_BOVIN_9913 are exactly identical! WARNING: Sequences tr_E2RDL8_E2RDL8_CANLF_9615 and tr_M3WG15_M3WG15_FELCA_9685 are exactly identical! WARNING: Sequences tr_E2RDL8_E2RDL8_CANLF_9615 and tr_A0A2U3VX95_A0A2U3VX95_ODORO_9708 are exactly identical! WARNING: Sequences tr_E2RDL8_E2RDL8_CANLF_9615 and tr_A0A2Y9KWT1_A0A2Y9KWT1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_E2RDL8_E2RDL8_CANLF_9615 and tr_A0A2Y9LME1_A0A2Y9LME1_DELLE_9749 are exactly identical! WARNING: Sequences tr_E2RDL8_E2RDL8_CANLF_9615 and tr_A0A2Y9SKD1_A0A2Y9SKD1_PHYCD_9755 are exactly identical! WARNING: Sequences tr_E2RDL8_E2RDL8_CANLF_9615 and tr_A0A383Z6H7_A0A383Z6H7_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A088AG06_A0A088AG06_APIME_7460 and tr_A0A2A3ERQ6_A0A2A3ERQ6_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A0E0FRR1_A0A0E0FRR1_ORYNI_4536 and tr_A2WU48_A2WU48_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0GNP6_A0A0E0GNP6_ORYNI_4536 and tr_A0A0E0NW48_A0A0E0NW48_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A5ABN9_A5ABN9_ASPNC_425011 and tr_A0A319ARJ3_A0A319ARJ3_9EURO_1450533 are exactly identical! WARNING: Sequences tr_F6W9M1_F6W9M1_MACMU_9544 and tr_G7PJG8_G7PJG8_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6W9M1_F6W9M1_MACMU_9544 and tr_A0A2K6DIG9_A0A2K6DIG9_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GEU6_F7GEU6_MACMU_9544 and tr_G7PF65_G7PF65_MACFA_9541 are exactly identical! WARNING: Sequences tr_G5APV2_G5APV2_HETGA_10181 and tr_A0A1U7TMV9_A0A1U7TMV9_TARSY_1868482 are exactly identical! WARNING: Sequences tr_F4P9S4_F4P9S4_BATDJ_684364 and tr_A0A177WVP8_A0A177WVP8_BATDE_403673 are exactly identical! WARNING: Sequences tr_F4WW66_F4WW66_ACREC_103372 and tr_A0A151XCD9_A0A151XCD9_9HYME_64791 are exactly identical! WARNING: Sequences tr_V2XGZ6_V2XGZ6_MONRO_1381753 and tr_A0A0W0FTU7_A0A0W0FTU7_9AGAR_221103 are exactly identical! WARNING: Sequences tr_A0A015K8P4_A0A015K8P4_9GLOM_1432141 and tr_A0A2I1GL02_A0A2I1GL02_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A044R887_A0A044R887_ONCVO_6282 and tr_A0A182EGZ2_A0A182EGZ2_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A096N559_A0A096N559_PAPAN_9555 and tr_A0A2K5LMG6_A0A2K5LMG6_CERAT_9531 are exactly identical! WARNING: Sequences tr_V4VZ98_V4VZ98_9ROSI_85681 and tr_A0A2H5PYW3_A0A2H5PYW3_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0V1CVH1_A0A0V1CVH1_TRIBR_45882 and tr_A0A0V0V846_A0A0V0V846_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A1S3NJV3_A0A1S3NJV3_SALSA_8030 and tr_B5X263_B5X263_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A226NEB5_A0A226NEB5_CALSU_9009 and tr_A0A226PA93_A0A226PA93_COLVI_9014 are exactly identical! WARNING: Duplicate sequences found: 36 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12872/4_raxmlng_ancestral/Q12872.raxml.reduced.phy Alignment comprises 1 partitions and 951 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 951 Gaps: 47.40 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12872/4_raxmlng_ancestral/Q12872.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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12872/3_mltree/Q12872.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 238 / 19040 [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: -233393.892259 [00:00:00 -233393.892259] Initial branch length optimization [00:00:01 -230419.779363] Model parameter optimization (eps = 0.100000) [00:00:53] Tree #1, final logLikelihood: -229629.487099 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.069204,0.295919) (0.056130,0.397104) (0.264636,0.609247) (0.610030,1.304859) 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: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12872/4_raxmlng_ancestral/Q12872.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12872/4_raxmlng_ancestral/Q12872.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12872/4_raxmlng_ancestral/Q12872.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q12872/4_raxmlng_ancestral/Q12872.raxml.log Analysis started: 02-Jun-2021 18:25:24 / finished: 02-Jun-2021 18:26:25 Elapsed time: 60.366 seconds Consumed energy: 4.167 Wh