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 12-Jul-2021 17:58:33 as follows: raxml-ng --ancestral --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N4F7/2_msa/Q8N4F7_nogap_msa.fasta --tree /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N4F7/3_mltree/Q8N4F7.raxml.bestTree_unrooted --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N4F7/4_raxmlng_ancestral/Q8N4F7 --threads 4 Analysis options: run mode: Ancestral state reconstruction start tree(s): user random seed: 1626101913 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/300621_run/phylogeny-snakemake/results/Q8N4F7/2_msa/Q8N4F7_nogap_msa.fasta [00:00:00] Loaded alignment with 653 taxa and 328 sites WARNING: Sequences tr_M3YG24_M3YG24_MUSPF_9669 and tr_A0A2Y9KV66_A0A2Y9KV66_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3HQC0_A0A2I3HQC0_NOMLE_61853 and tr_K7DCB3_K7DCB3_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3HQC0_A0A2I3HQC0_NOMLE_61853 and sp_Q9BV68_RN126_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3HQC0_A0A2I3HQC0_NOMLE_61853 and tr_F7F3B5_F7F3B5_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3HQC0_A0A2I3HQC0_NOMLE_61853 and tr_A0A0A0MV20_A0A0A0MV20_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3HQC0_A0A2I3HQC0_NOMLE_61853 and tr_A0A2K5P2K7_A0A2K5P2K7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3HQC0_A0A2I3HQC0_NOMLE_61853 and tr_A0A2K6D4A5_A0A2K6D4A5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3HRX1_A0A2I3HRX1_NOMLE_61853 and tr_F7EE81_F7EE81_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3HRX1_A0A2I3HRX1_NOMLE_61853 and tr_M3W3V2_M3W3V2_FELCA_9685 are exactly identical! WARNING: Sequences tr_A0A2I3HRX1_A0A2I3HRX1_NOMLE_61853 and tr_A0A096MMB2_A0A096MMB2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3HRX1_A0A2I3HRX1_NOMLE_61853 and tr_A0A0D9QW22_A0A0D9QW22_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3HRX1_A0A2I3HRX1_NOMLE_61853 and tr_A0A2K6AS20_A0A2K6AS20_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3HRX1_A0A2I3HRX1_NOMLE_61853 and tr_A0A2K6AEM6_A0A2K6AEM6_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2NEJ4_H2NEJ4_PONAB_9601 and tr_H2R3C0_H2R3C0_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2NEJ4_H2NEJ4_PONAB_9601 and sp_Q9H920_RN121_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2NEJ4_H2NEJ4_PONAB_9601 and tr_A0A2R9AR76_A0A2R9AR76_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2PBQ8_H2PBQ8_PONAB_9601 and tr_A0A096MS08_A0A096MS08_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2PBQ8_H2PBQ8_PONAB_9601 and tr_A0A0D9RGK1_A0A0D9RGK1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2PBQ8_H2PBQ8_PONAB_9601 and tr_A0A2K6A6Z9_A0A2K6A6Z9_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2PBQ8_H2PBQ8_PONAB_9601 and tr_A0A2R9BEY4_A0A2R9BEY4_PANPA_9597 are exactly identical! WARNING: Sequences tr_W5P3L5_W5P3L5_SHEEP_9940 and sp_Q0VD51_RNF13_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A3B5RBK3_A0A3B5RBK3_XIPMA_8083 and tr_A0A096M9B3_A0A096M9B3_POEFO_48698 are exactly identical! WARNING: Sequences tr_I1NNT6_I1NNT6_ORYGL_4538 and tr_A0A0D3EPV4_A0A0D3EPV4_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_H0YQT9_H0YQT9_TAEGU_59729 and tr_A0A218UFN0_A0A218UFN0_9PASE_299123 are exactly identical! WARNING: Sequences tr_F4WQ12_F4WQ12_ACREC_103372 and tr_A0A195ECT3_A0A195ECT3_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A0E0MXK7_A0A0E0MXK7_ORYRU_4529 and tr_A0A0D9YA43_A0A0D9YA43_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A8XXA9_A8XXA9_CAEBR_6238 and tr_A0A2G5UJK0_A0A2G5UJK0_9PELO_1611254 are exactly identical! WARNING: Sequences tr_D2HM63_D2HM63_AILME_9646 and tr_A0A2Y9JN45_A0A2Y9JN45_ENHLU_391180 are exactly identical! WARNING: Sequences tr_D2HM63_D2HM63_AILME_9646 and tr_A0A384DEL1_A0A384DEL1_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2I2UIC9_A0A2I2UIC9_FELCA_9685 and tr_A0A2U3VKQ6_A0A2U3VKQ6_ODORO_9708 are exactly identical! WARNING: Sequences tr_M4EQB1_M4EQB1_BRARP_51351 and tr_A0A078JPG3_A0A078JPG3_BRANA_3708 are exactly identical! WARNING: Sequences tr_A0A067FGN6_A0A067FGN6_CITSI_2711 and tr_V4UEM0_V4UEM0_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067FGN6_A0A067FGN6_CITSI_2711 and tr_A0A2H5PG43_A0A2H5PG43_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A087XDT8_A0A087XDT8_POEFO_48698 and tr_A0A096LVW1_A0A096LVW1_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A0Q3PWS1_A0A0Q3PWS1_AMAAE_12930 and tr_A0A091W2B7_A0A091W2B7_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091WIS7_A0A091WIS7_NIPNI_128390 and tr_A0A093HR27_A0A093HR27_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091WIS7_A0A091WIS7_NIPNI_128390 and tr_A0A0A0B2I3_A0A0A0B2I3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V0WK23_A0A0V0WK23_9BILA_92179 and tr_A0A0V1L595_A0A0V1L595_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A164T7A7_A0A164T7A7_9HOMO_1314777 and tr_A0A166A4Z9_A0A166A4Z9_9HOMO_1314776 are exactly identical! WARNING: Sequences tr_A0A1S4CLR6_A0A1S4CLR6_TOBAC_4097 and tr_A0A1U7X5L3_A0A1U7X5L3_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3M042_A0A1S3M042_SALSA_8030 and tr_A0A060XBD4_A0A060XBD4_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3QCD9_A0A1S3QCD9_SALSA_8030 and tr_A0A1S3RZE9_A0A1S3RZE9_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1U7TGH6_A0A1U7TGH6_TARSY_1868482 and tr_A0A2Y9TBE7_A0A2Y9TBE7_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4B9L0_A0A2U4B9L0_TURTR_9739 and tr_A0A2Y9NTW9_A0A2Y9NTW9_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BPE8_A0A2U4BPE8_TURTR_9739 and tr_A0A2Y9MH57_A0A2Y9MH57_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BPE8_A0A2U4BPE8_TURTR_9739 and tr_A0A2Y9S7R6_A0A2Y9S7R6_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9MW08_A0A2Y9MW08_DELLE_9749 and tr_A0A2Y9THN9_A0A2Y9THN9_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 47 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N4F7/4_raxmlng_ancestral/Q8N4F7.raxml.reduced.phy Alignment comprises 1 partitions and 328 sites Partition 0: noname Model: LG4X+R4 Alignment sites: 328 Gaps: 35.29 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N4F7/4_raxmlng_ancestral/Q8N4F7.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/300621_run/phylogeny-snakemake/results/Q8N4F7/3_mltree/Q8N4F7.raxml.bestTree_unrooted [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 82 / 6560 [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: -97195.886814 [00:00:00 -97195.886814] Initial branch length optimization [00:00:00 -94147.416941] Model parameter optimization (eps = 0.100000) [00:00:29] Tree #1, final logLikelihood: -93988.251804 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.085468,0.242851) (0.153718,0.503250) (0.558367,0.940523) (0.202448,1.860868) 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/300621_run/phylogeny-snakemake/results/Q8N4F7/4_raxmlng_ancestral/Q8N4F7.raxml.ancestralProbs Reconstructed ancestral sequences saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N4F7/4_raxmlng_ancestral/Q8N4F7.raxml.ancestralStates Node-labeled tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N4F7/4_raxmlng_ancestral/Q8N4F7.raxml.ancestralTree Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8N4F7/4_raxmlng_ancestral/Q8N4F7.raxml.log Analysis started: 12-Jul-2021 17:58:33 / finished: 12-Jul-2021 17:59:05 Elapsed time: 31.937 seconds Consumed energy: 1.243 Wh